Publications 2026

@article{zhou_early_2026,
	title = {{EARLY} {ABORTION} 1 is an evolutionary conserved gene required for plant reproduction},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag142},
	doi = {10.1093/jxb/erag142},
	abstract = {The functions of approximately one-third of the proteins in the model plant Arabidopsis thaliana remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.},
	urldate = {2026-03-27},
	journal = {Journal of Experimental Botany},
	author = {Zhou, Jingjing and Wang, Wei and Zhang, Li and Bruce, Ylva and Zhu, Shaochun and Mateus, André and Niittylä, Totte},
	month = mar,
	year = {2026},
	pages = {erag142},
}

The functions of approximately one-third of the proteins in the model plant Arabidopsis thaliana remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.

@article{moazzami_farida_dopamine_2026,
	title = {Dopamine modulates antioxidant and phenolic responses to alleviate nickel stress in {Salvia} officinalis},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08365-5},
	doi = {10.1186/s12870-026-08365-5},
	abstract = {Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.},
	language = {en},
	number = {1},
	urldate = {2026-03-27},
	journal = {BMC Plant Biology},
	author = {Moazzami Farida, Seyed Hamed and Rahmani, Nosrat and Taghizadeh, Marzieh and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2026},
	keywords = {Antioxidant defense, Dopamine, Heavy metal, Nickel stress, Phenolic metabolism, Salvia officinalis l},
	pages = {491},
}

Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.

@article{wang_recurrent_2026,
	title = {Recurrent sex chromosome turnover mediated by distinct {ARR17} and {PISTILLATA} duplications in willows},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-026-04026-w},
	doi = {10.1186/s13059-026-04026-w},
	abstract = {Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.},
	language = {en},
	urldate = {2026-03-20},
	journal = {Genome Biology},
	author = {Wang, Yuàn and Xue, Zhi-Qing and Zhang, Ren-Gang and Zhu, Zhi-Ying and Hörandl, Elvira and Wang, Xiao-Ru and Mao, Yan-Fei and Charlesworth, Deborah and He, Li},
	month = mar,
	year = {2026},
	keywords = {Pericentromeric regions, Recombination landscape, Salix, Sex chromosome turnovers, Sex determination, Translocation},
}

Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.

@article{eklof_contrasting_2026,
	title = {Contrasting {Patterns} of {Local} {Adaptation} and {Adaptive} {Potential} {Under} {Climate} {Change} for {Old}-{Growth} and {Planted} {Stands} of {Norway} {Spruce} ({Picea} abies)},
	volume = {19},
	copyright = {© 2026 The Author(s). Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.70217},
	doi = {10.1111/eva.70217},
	abstract = {Genetic diversity is a key prerequisite for adaptation to changing environments. Maintaining genetic diversity in forest trees is crucial amid climate change, given their long generation times. Forest management practices can affect the genetic diversity of forest ecosystems through selective felling or reforestation strategies following harvests. To assess how managed forests respond to climate-driven changes, we investigated patterns of genetic diversity and local adaptation by contrasting old-growth and recently planted stands of Norway spruce (Picea abies). We assess both neutral and adaptive genetic variation by sequencing pooled samples collected from 45 first stands across northern Sweden. Our results reveal no significant differences in overall genetic diversity between natural and planted populations, indicating that current forest management practices have not substantially reduced genetic variation. Analyses of adaptive variation demonstrate strong signatures of local adaptation in old-growth populations, with clear correlations between genetic and environmental distances. In contrast, planted stands show weaker adaptive signals and are also at greater risk of non-adaptiveness under future climate scenarios. While current forest management practices preserve much of the neutral genetic diversity necessary for long-term forest health, our findings highlight the importance of conserving and promoting adaptive genetic variation available in old-growth stands to ensure resilience against ongoing climate change.},
	language = {en},
	number = {3},
	urldate = {2026-03-20},
	journal = {Evolutionary Applications},
	author = {Eklöf, Helena and Bernhardsson, Carolina and Ingvarsson, Pär K.},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.70217},
	keywords = {Norway spruce, forest regeneration, forestry, genetic differentiation, genetic diversity},
	pages = {e70217},
}

Genetic diversity is a key prerequisite for adaptation to changing environments. Maintaining genetic diversity in forest trees is crucial amid climate change, given their long generation times. Forest management practices can affect the genetic diversity of forest ecosystems through selective felling or reforestation strategies following harvests. To assess how managed forests respond to climate-driven changes, we investigated patterns of genetic diversity and local adaptation by contrasting old-growth and recently planted stands of Norway spruce (Picea abies). We assess both neutral and adaptive genetic variation by sequencing pooled samples collected from 45 first stands across northern Sweden. Our results reveal no significant differences in overall genetic diversity between natural and planted populations, indicating that current forest management practices have not substantially reduced genetic variation. Analyses of adaptive variation demonstrate strong signatures of local adaptation in old-growth populations, with clear correlations between genetic and environmental distances. In contrast, planted stands show weaker adaptive signals and are also at greater risk of non-adaptiveness under future climate scenarios. While current forest management practices preserve much of the neutral genetic diversity necessary for long-term forest health, our findings highlight the importance of conserving and promoting adaptive genetic variation available in old-growth stands to ensure resilience against ongoing climate change.

@article{cainzos_loss_2026,
	title = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}: {Sustained} {Non}-{Photochemical} {Quenching} in the {Absence} of {PsbS} and {Zeaxanthin}},
	copyright = {© 2026 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.70477},
	doi = {10.1111/pce.70477},
	abstract = {Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.},
	language = {en},
	urldate = {2026-03-13},
	journal = {Plant, Cell \& Environment},
	author = {Cainzos, Maximiliano and Hu, Chen and Pissolato, Maria Dolores and Fataftah, Nazeer and Nanda, Sanchali and Jansson, Stefan},
	month = mar,
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.70477},
	keywords = {NPQ, high light, new emitting species development, photoinhibition, photosynthesis: carbon reactions, photosynthesis: electron transport, sustained quenching},
}

Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.

@article{alonso-serra_growth_2026,
	title = {On growth and flow: hydraulic aspects of aboveground meristems},
	volume = {249},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {On growth and flow},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70713},
	doi = {10.1111/nph.70713},
	abstract = {Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.},
	language = {en},
	number = {2},
	urldate = {2026-03-18},
	journal = {New Phytologist},
	author = {Alonso-Serra, Juan},
	year = {2026},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70713},
	keywords = {biomechanics, cambium, hydraulics, meristem, shoot apical meristem, water},
	pages = {722--728},
}

Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.

@article{kasige_interactions_2026,
	title = {Interactions between beneficial fungi and plant silicon: {A} review},
	volume = {114},
	copyright = {© 2025 The Author(s). Journal of Ecology © 2025 British Ecological Society.},
	issn = {1365-2745},
	shorttitle = {Interactions between beneficial fungi and plant silicon},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.70207},
	doi = {10.1111/1365-2745.70207},
	abstract = {Silicon (Si) accumulation in plants often plays an important functional role by alleviating the adverse impacts of the plant antagonists (e.g. invertebrate herbivores). Mutualistic associations with beneficial fungi, such as below-ground arbuscular mycorrhizal (AM) fungi and above-ground Epichloë endophytes, play similar roles for plant protection. Evidence suggests that beneficial fungi significantly influence Si uptake, often increasing Si in plant tissues while Si supplementation may in turn enhance fungal colonisation. However, this two-way association remains poorly understood due to the fragmented nature of existing literature. We assess the current state of knowledge on interactions between Si and beneficial fungi by extracting and comparing effect sizes (Cohen's d) from peer-reviewed literature for various reported relationships. We aim to understand the (i) interactions between Si and beneficial fungi, (ii) potential mechanisms underlying their interactions and (iii) role of Si-fungal interactions in enhancing plant resilience to environmental stresses. The Glomeraceae AM family was the most frequently investigated and was generally associated with increased Si accumulation in plants (overall effect size, d = 0.7). Additionally, Si supplementation was commonly reported to have a positive effect, with a modest overall increase in AM fungal colonisation (overall effect size, d = 0.3). These observations are often associated with changes in plant growth, morphology, physiology and chemistry by either Si or fungi. The literature covering Epichloë endophytes was limited and showed highly variable, strain-specific trends. Interactions between Si supply and beneficial fungi have mostly been studied in the context of abiotic stresses with limited focus on biotic antagonists (only nine studies). However, the extent to which Si and beneficial fungi increased plant resistance to stresses suggests that their interactions could play a significant role in plant community dynamics, potentially disadvantaging plant species that lack these traits. Synthesis. This review aims to help predict how beneficial fungi may interact with Si supply to enhance resistance to environmental stresses. Overall, Si supply and beneficial fungi seem to work ‘synergistically’ especially when Si availability is low, or when the plant species is a low Si accumulator. Finally, we identified potential avenues for future research based on existing knowledge and key knowledge gaps.},
	language = {en},
	number = {1},
	urldate = {2026-03-17},
	journal = {Journal of Ecology},
	author = {Kasige, Ramalka Heshani and Cibils-Stewart, Ximena and Frew, Adam and Johnson, Scott Nicholas},
	year = {2026},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.70207},
	keywords = {Epichloë endophytes, arbuscular mycorrhizal fungi, silica, silicon accumulation, silicon uptake},
	pages = {e70207},
}

Silicon (Si) accumulation in plants often plays an important functional role by alleviating the adverse impacts of the plant antagonists (e.g. invertebrate herbivores). Mutualistic associations with beneficial fungi, such as below-ground arbuscular mycorrhizal (AM) fungi and above-ground Epichloë endophytes, play similar roles for plant protection. Evidence suggests that beneficial fungi significantly influence Si uptake, often increasing Si in plant tissues while Si supplementation may in turn enhance fungal colonisation. However, this two-way association remains poorly understood due to the fragmented nature of existing literature. We assess the current state of knowledge on interactions between Si and beneficial fungi by extracting and comparing effect sizes (Cohen's d) from peer-reviewed literature for various reported relationships. We aim to understand the (i) interactions between Si and beneficial fungi, (ii) potential mechanisms underlying their interactions and (iii) role of Si-fungal interactions in enhancing plant resilience to environmental stresses. The Glomeraceae AM family was the most frequently investigated and was generally associated with increased Si accumulation in plants (overall effect size, d = 0.7). Additionally, Si supplementation was commonly reported to have a positive effect, with a modest overall increase in AM fungal colonisation (overall effect size, d = 0.3). These observations are often associated with changes in plant growth, morphology, physiology and chemistry by either Si or fungi. The literature covering Epichloë endophytes was limited and showed highly variable, strain-specific trends. Interactions between Si supply and beneficial fungi have mostly been studied in the context of abiotic stresses with limited focus on biotic antagonists (only nine studies). However, the extent to which Si and beneficial fungi increased plant resistance to stresses suggests that their interactions could play a significant role in plant community dynamics, potentially disadvantaging plant species that lack these traits. Synthesis. This review aims to help predict how beneficial fungi may interact with Si supply to enhance resistance to environmental stresses. Overall, Si supply and beneficial fungi seem to work ‘synergistically’ especially when Si availability is low, or when the plant species is a low Si accumulator. Finally, we identified potential avenues for future research based on existing knowledge and key knowledge gaps.

@article{huang_contrasting_2026,
	title = {Contrasting strategies of two \textit{{Camellia} oleifera} cultivars in shaping arbuscular mycorrhizal fungi communities under different phosphorus forms},
	volume = {128},
	issn = {1164-5563},
	url = {https://www.sciencedirect.com/science/article/pii/S1164556326000129},
	doi = {10.1016/j.ejsobi.2026.103814},
	abstract = {Phosphorus (P) availability regulates the arbuscular mycorrhizal fungi (AMF) symbiosis, but the distinct effects of different P forms (soluble, insoluble, organic) and host plant genotypes on AMF communities remain underexplored. Using Camellia oleifera cultivars with contrasting P-use efficiencies (low-P-sensitive CL3 and low-P-tolerant CL40), we examined how P forms and cultivar identity shape AMF communities and their functional linkages to plant growth and soil nutrients. The results showed that soluble inorganic P (SP) maximized plant height and biomass but suppressed AMF diversity and simplified co-occurrence networks. In contrast, insoluble inorganic P (IP) enhanced AMF colonization rates and stabilized microbial interactions. The low-P-sensitive CL3 hosted a higher Chao1 index under P limitation, suggesting compensatory recruitment for P acquisition, while CL40 exhibited stronger soil P activation and maintained complex AMF networks. Glomus and Paraglomus were identified as core taxa in the rhizosphere AMF networks of C. oleifera. RDA and Mantel analyses showed that variation in plant growth and root traits was aligned with AMF characteristics, particularly colonization and core taxa (Glomus, Paraglomus), and strongly associated with soil nutrients, with SP treatment reducing mycorrhizal dependence and shifting associations toward Paraglomus. These insights inform targeted cultivar selection and phosphorus management to optimize C. oleifera production and maintain soil health.},
	urldate = {2026-03-17},
	journal = {European Journal of Soil Biology},
	author = {Huang, Yuxuan and You, Xin and Frew, Adam and Wu, Fei and Zhang, Linping and Liu, Xinping and Xing, Jiaoping},
	month = mar,
	year = {2026},
	keywords = {Arbuscular mycorrhizal fungi diversity, Cultivar, Phosphorus forms, Rhizosphere},
	pages = {103814},
}

Phosphorus (P) availability regulates the arbuscular mycorrhizal fungi (AMF) symbiosis, but the distinct effects of different P forms (soluble, insoluble, organic) and host plant genotypes on AMF communities remain underexplored. Using Camellia oleifera cultivars with contrasting P-use efficiencies (low-P-sensitive CL3 and low-P-tolerant CL40), we examined how P forms and cultivar identity shape AMF communities and their functional linkages to plant growth and soil nutrients. The results showed that soluble inorganic P (SP) maximized plant height and biomass but suppressed AMF diversity and simplified co-occurrence networks. In contrast, insoluble inorganic P (IP) enhanced AMF colonization rates and stabilized microbial interactions. The low-P-sensitive CL3 hosted a higher Chao1 index under P limitation, suggesting compensatory recruitment for P acquisition, while CL40 exhibited stronger soil P activation and maintained complex AMF networks. Glomus and Paraglomus were identified as core taxa in the rhizosphere AMF networks of C. oleifera. RDA and Mantel analyses showed that variation in plant growth and root traits was aligned with AMF characteristics, particularly colonization and core taxa (Glomus, Paraglomus), and strongly associated with soil nutrients, with SP treatment reducing mycorrhizal dependence and shifting associations toward Paraglomus. These insights inform targeted cultivar selection and phosphorus management to optimize C. oleifera production and maintain soil health.

@article{kyaschenko_consistent_2026,
	title = {Consistent {Species} {Richness} {Patterns} but {Not} {Richness} {Estimates} {Based} on {Both} {ASV} and {OTU} {Inference} {Methods} on {ITS2}-{Based} {Soil} {Fungal} {Communities}},
	volume = {8},
	issn = {2637-4943},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/edn3.70246},
	doi = {10.1002/edn3.70246},
	abstract = {Fungi play essential roles in key ecosystem functions and processes, yet they often occur in inconspicuous, species-rich, and complex communities that remain difficult to study. Studies of fungal communities based on DNA extracted from environmental samples commonly rely on clustering sequence reads into units of diversity, followed by taxonomic identification and, in some cases, linkage to ecological traits. In this study, we evaluated how two clustering approaches—amplicon sequence variants (ASVs) and operational taxonomic units (OTUs)—affect the characterization of fungal communities. Despite minor differences, both approaches recovered consistent taxonomic patterns and community structure. Although both methods produced a similar total number of sequence clusters, they differed in representation of fungal community composition. All ASV representative sequences matched OTU representative sequences with at least 92.2\% similarity, whereas several rare OTUs showed low similarity to ASV reads, suggesting differences in the detection of low-abundance taxa. However, only a small fraction of OTU reads ({\textless} 0.1\%) lacked a corresponding ASV, indicating that ASVs captured nearly all OTU-defined taxa. In contrast, 14\% of ASV reads assigned to species hypotheses (SHs) did not match any OTU reads assigned to SHs, whereas only 1.3\% of OTU SH-assigned reads lacked a corresponding ASV match. ASVs generally provided higher resolution than OTUs, as abundant SHs were often represented by multiple ASVs, suggesting that ASVs capture intraspecific diversity. Consequently, ASVs should not be used as direct species proxies but instead require post hoc grouping to reflect species-level diversity. OTUs-based community composition aligned more clearly with soil properties, particularly the N:C ratio. Overall, both approaches provided a similar overview of broad-scale species richness. The choice between two clustering methods depends on the research question and the desired level of taxonomic resolution, and our results provide little support for the claim that ASVs should categorically replace taxonomic units in marker-gene data analysis.},
	language = {en},
	number = {1},
	urldate = {2026-03-16},
	journal = {Environmental DNA},
	author = {Kyaschenko, Julia and Tångrot, Jeanette and Dahlberg, Anders and Lindahl, Björn D. and Rosling, Anna},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.70246},
	keywords = {DNA barcoding, community dynamics, ecosystem, fungi, high-throughput nucleotide sequencing, molecular taxonomy, soil biodiversity, species specificity, taxonomy},
	pages = {e70246},
}

Fungi play essential roles in key ecosystem functions and processes, yet they often occur in inconspicuous, species-rich, and complex communities that remain difficult to study. Studies of fungal communities based on DNA extracted from environmental samples commonly rely on clustering sequence reads into units of diversity, followed by taxonomic identification and, in some cases, linkage to ecological traits. In this study, we evaluated how two clustering approaches—amplicon sequence variants (ASVs) and operational taxonomic units (OTUs)—affect the characterization of fungal communities. Despite minor differences, both approaches recovered consistent taxonomic patterns and community structure. Although both methods produced a similar total number of sequence clusters, they differed in representation of fungal community composition. All ASV representative sequences matched OTU representative sequences with at least 92.2% similarity, whereas several rare OTUs showed low similarity to ASV reads, suggesting differences in the detection of low-abundance taxa. However, only a small fraction of OTU reads (\textless 0.1%) lacked a corresponding ASV, indicating that ASVs captured nearly all OTU-defined taxa. In contrast, 14% of ASV reads assigned to species hypotheses (SHs) did not match any OTU reads assigned to SHs, whereas only 1.3% of OTU SH-assigned reads lacked a corresponding ASV match. ASVs generally provided higher resolution than OTUs, as abundant SHs were often represented by multiple ASVs, suggesting that ASVs capture intraspecific diversity. Consequently, ASVs should not be used as direct species proxies but instead require post hoc grouping to reflect species-level diversity. OTUs-based community composition aligned more clearly with soil properties, particularly the N:C ratio. Overall, both approaches provided a similar overview of broad-scale species richness. The choice between two clustering methods depends on the research question and the desired level of taxonomic resolution, and our results provide little support for the claim that ASVs should categorically replace taxonomic units in marker-gene data analysis.

@article{bao_chromosome-level_2026,
	title = {A chromosome-level genome assembly of \textit{{Platycladus} orientalis} and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346226001227},
	doi = {10.1016/j.xplc.2026.101814},
	abstract = {Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. How TEs are involved in shaping the coding space of gymnosperm genomes is one remaining key question. Herein, we generate the high-quality genome assembly for a keystone conifer, Platycladus orientalis, with a contig N50 of 57.54 Mb (the highest continuity currently available) to investigate the role of TEs. Comparative genomics affirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing the complex interactions among recurrent TE proliferation, low removal rate, and DNA methylation silencing. Computationally detectable TE-mediated gene duplication and pseudogenization provide the genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of 400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captive exon fragments. Genes from which the fragment has been captured (donor genes) show significantly higher levels of exon methylation compared to genes without the capture by TEs (free genes), while syntenic donor genes exhibit lower levels of silencing response than non-syntenic donor genes. This study provides important genomic resources and offers insights into the evolutionary patterns and principles underlying the giant size and complexity of gymnosperm genomes.},
	urldate = {2026-03-13},
	journal = {Plant Communications},
	author = {Bao, Yu-Tao and Zhang, Ren-Gang and Liu, Hui and Li, Zhi-Chao and Jiao, Si-Qian and Jia, Kai-Hua and Zhou, Shan-Shan and Nie, Shuai and Yan, Xue-Mei and Shi, Tian-Le and Tian, Xue-Chan and Zhao, Shi-Wei and Kong, Lei and Chen, Zhao-Yang and Ma, Hai-Yao and Yang, Xiao-Lei and Chen, Charles and El-Kassaby, Yousry Aly and Porth, Ilga and Wang, Xiao-Ru and Mao, Jian-Feng and Zhao, Wei},
	month = mar,
	year = {2026},
	keywords = {gene duplication, gene fragment capture, genome expansion, gymnosperms, pseudogenization, transposable elements},
	pages = {101814},
}

Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. How TEs are involved in shaping the coding space of gymnosperm genomes is one remaining key question. Herein, we generate the high-quality genome assembly for a keystone conifer, Platycladus orientalis, with a contig N50 of 57.54 Mb (the highest continuity currently available) to investigate the role of TEs. Comparative genomics affirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing the complex interactions among recurrent TE proliferation, low removal rate, and DNA methylation silencing. Computationally detectable TE-mediated gene duplication and pseudogenization provide the genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of 400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captive exon fragments. Genes from which the fragment has been captured (donor genes) show significantly higher levels of exon methylation compared to genes without the capture by TEs (free genes), while syntenic donor genes exhibit lower levels of silencing response than non-syntenic donor genes. This study provides important genomic resources and offers insights into the evolutionary patterns and principles underlying the giant size and complexity of gymnosperm genomes.

@article{muraro_early_2026,
	title = {Early establishment of fast-growing tree species on forest land and forested arable land in southern {Sweden}: {Implications} for forest diversification},
	volume = {609},
	issn = {0378-1127},
	shorttitle = {Early establishment of fast-growing tree species on forest land and forested arable land in southern {Sweden}},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112726001404},
	doi = {10.1016/j.foreco.2026.123642},
	abstract = {Climate change and pest outbreaks are increasingly threatening conifer-dominated forests in Northern Europe, highlighting the need for greater species diversity to improve resilience. This study assessed early establishment success of six tree species: European aspen (Populus tremula), hybrid aspen (P. tremula × P. tremuloides), silver birch (Betula pendula), Norway spruce (Picea abies), Scots pine (Pinus sylvestris), and hybrid poplar (P. trichocarpa × P. maximowiczii), across seven sites in southern Sweden. Sites were categorized as either forest land (continuous forest cover {\textgreater}100 years) or forested arable land (former arable land afforested with Norway spruce for 40–70 years). Over three years, we monitored survival, height, and diameter growth. All experimental sites were fenced to exclude browsing. Wood ash was applied to a subset of hybrid poplars to assess its effect on establishment in acidic soils. Our results showed that hybrid aspen, birch, and European aspen had high survival and growth on forest land. On forested arable land, untreated Norway spruce, Scots pine, and hybrid poplar showed low survival, likely due to competition from dense vegetation. However, ash-treated poplar improved survival to approximately 80\% and showed strong growth on forested arable sites. Principal Component Analysis indicated overall higher establishment success on forest land for most species, whereas hybrid poplar performed similarly on forest and forested arable land when wood ash was applied. These findings underscore the importance of matching species to site conditions during early establishment and provide empirical evidence to inform species selection for forest regeneration under similar site conditions in southern Sweden.},
	urldate = {2026-03-13},
	journal = {Forest Ecology and Management},
	author = {Muraro, Luca and Robinson, Kathryn and Liziniewicz, Mateusz and Böhlenius, Henrik},
	month = jun,
	year = {2026},
	keywords = {Broadleaved trees, Forest land, Forest regeneration, Forested arable land, Populus, Species diversification, Tree establishment},
	pages = {123642},
}

Climate change and pest outbreaks are increasingly threatening conifer-dominated forests in Northern Europe, highlighting the need for greater species diversity to improve resilience. This study assessed early establishment success of six tree species: European aspen (Populus tremula), hybrid aspen (P. tremula × P. tremuloides), silver birch (Betula pendula), Norway spruce (Picea abies), Scots pine (Pinus sylvestris), and hybrid poplar (P. trichocarpa × P. maximowiczii), across seven sites in southern Sweden. Sites were categorized as either forest land (continuous forest cover \textgreater100 years) or forested arable land (former arable land afforested with Norway spruce for 40–70 years). Over three years, we monitored survival, height, and diameter growth. All experimental sites were fenced to exclude browsing. Wood ash was applied to a subset of hybrid poplars to assess its effect on establishment in acidic soils. Our results showed that hybrid aspen, birch, and European aspen had high survival and growth on forest land. On forested arable land, untreated Norway spruce, Scots pine, and hybrid poplar showed low survival, likely due to competition from dense vegetation. However, ash-treated poplar improved survival to approximately 80% and showed strong growth on forested arable sites. Principal Component Analysis indicated overall higher establishment success on forest land for most species, whereas hybrid poplar performed similarly on forest and forested arable land when wood ash was applied. These findings underscore the importance of matching species to site conditions during early establishment and provide empirical evidence to inform species selection for forest regeneration under similar site conditions in southern Sweden.

@article{wahl_plant_2026,
	title = {The plant energy management machinery: an essential hub for stress resilience and developmental dynamics with great potential for crop improvement},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {The plant energy management machinery},
	url = {https://doi.org/10.1093/jxb/erag032},
	doi = {10.1093/jxb/erag032},
	abstract = {Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.},
	number = {5},
	urldate = {2026-03-10},
	journal = {Journal of Experimental Botany},
	author = {Wahl, Vanessa and Hanson, Johannes and Menand, Benoît},
	month = mar,
	year = {2026},
	pages = {1357--1361},
}

Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.

@article{mahawar_straw_2026,
	title = {Straw {Mulching} {Differentially} {Shapes} the {Structure} and {Function} of {Below}-{Ground} {Bacterial} {Communities} in {Potato} {Depending} on {eDNA} {Source} and {Cultivar}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by New Phytologist Foundation and John Wiley \& Sons Ltd.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70131},
	doi = {10.1002/pei3.70131},
	abstract = {Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Plant-Environment Interactions},
	author = {Mahawar, Lovely and Mishra, Arti and Tsitouri, Angeliki and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70131},
	keywords = {bacterial communities, cv King Edward, cv Mandel, illumina amplicon sequencing, metabarcoding},
	pages = {e70131},
}

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

@article{brun_chip-ms_2026,
	title = {{ChIP}-{MS} in {Plant} {Systems}: {Mapping} the {H3K27ac} {Proteome} {During} the {Greening} {Process}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	shorttitle = {{ChIP}-{MS} in {Plant} {Systems}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70797},
	doi = {10.1111/ppl.70797},
	abstract = {We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Physiologia Plantarum},
	author = {Brun, Alexis and Quevedo, Marti and Sterling, Luis A. and Dekkers, Dick H. W. and Demmers, Jeroen and Hudson, Elton Paul and Strand, Åsa},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70797},
	keywords = {MS, chromatin, histone modifications, photosynthesis},
	pages = {e70797},
}

We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.

@article{han_development_2026,
	title = {Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in {Salix} suchowensis},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-026-12690-2},
	doi = {10.1186/s12864-026-12690-2},
	abstract = {Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.},
	language = {en},
	urldate = {2026-03-09},
	journal = {BMC Genomics},
	author = {Han, Yu and Gu, Shaobo and Zhu, Mingjia and Liu, Wei and Feng, Landi and Yin, Tongming and Gao, Xuemeng and Zan, Yanjun and Huang, Rui and Ji, Yan and Liu, Jianquan},
	month = mar,
	year = {2026},
	keywords = {Genome-wide association study, Genomic selection, Ground diameter, Liquid-phase probe array, Plant height},
}

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

@article{pinosio_forgenius_2026,
	title = {The {FORGENIUS} {Genomic} {Resources}: {New} {Genotyping} {Tools} and {Genomic} {Data} for 23 {Forest} {Tree} {Species} and {Their} {Genetic} {Conservation} {Units}},
	volume = {26},
	issn = {1755-0998},
	shorttitle = {The {FORGENIUS} {Genomic} {Resources}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.70115},
	doi = {10.1111/1755-0998.70115},
	abstract = {Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.},
	language = {en},
	number = {3},
	urldate = {2026-03-09},
	journal = {Molecular Ecology Resources},
	author = {Pinosio, Sara and Bagnoli, Francesca and Avanzi, Camilla and Castellani, Maria B. and Frascella, Arcangela and McEvoy, Susan L. and Olsson, Sanna and Spanu, Ilaria and Vajana, Elia and Consortium, the FORGENIUS and González-Martínez, Santiago C. and Pyhäjärvi, Tanja and Scotti, Ivan and Vendramin, Giovanni G. and Piotti, Andrea},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70115},
	keywords = {forest tree species, genetic conservation units, genetic diversity, genetic monitoring, single primer enrichment technology, targeted genotyping},
	pages = {e70115},
}

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.

@article{klaminder_perspective_2026,
	title = {Perspective: {The} enigmatic extirpation of {Russian} larch from {Fennoscandia} and its relevance to modern forestry},
	volume = {608},
	issn = {0378-1127},
	shorttitle = {Perspective},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112726000976},
	doi = {10.1016/j.foreco.2026.123599},
	abstract = {For more than two centuries, Russian larch (Larix sibirica; Larix sukaczewii; Larix archangelica) was considered an alien species within Fennoscandia forestry. Findings of ancient alpine macrofossils led the Swedish Forest Agency to a policy shift where the Russian larch became recognized as part of the native flora. Despite the ongoing use of larch within Fennoscandian forestry, we lack a thorough discussion about its historic extirpation from this region and the possibility that it may happen again. In this perspective, we highlight that paleoecological studies indicate that Russian larch existed not only in alpine regions of Fennoscandia as previously suggested, but also in boreal areas of Sweden, Finland and Latvia. We identified a longitudinal trend where larch populations disappeared from western alpine habitats in Early Holocene but lingered until the last millennia in easter part of Finland. Our empirical analyses of forest experiments suggest that Russian larch has a growth advantage against Scots pine (Pinus sylverstris) and Norway spruce (Picea abies) across contemporary cold Fennoscandian climates, making it unlikely that Russian larch was extirpated simply due to negative growth effects from a colder climate occurring after the Early/Mid Holocene thermal optimum. We highlight that the driver(s) behind the enigmatic extirpation of Russian larch remain unresolved but should warrant attention given the current interest for Russian larch within Fennoscandian forestry.},
	urldate = {2026-02-20},
	journal = {Forest Ecology and Management},
	author = {Klaminder, Jonatan and Klingberg, Adam and Jerand, Philip},
	month = may,
	year = {2026},
	keywords = {Finland, Norway, Silviculture, Sweden, Vegetation history},
	pages = {123599},
}

For more than two centuries, Russian larch (Larix sibirica; Larix sukaczewii; Larix archangelica) was considered an alien species within Fennoscandia forestry. Findings of ancient alpine macrofossils led the Swedish Forest Agency to a policy shift where the Russian larch became recognized as part of the native flora. Despite the ongoing use of larch within Fennoscandian forestry, we lack a thorough discussion about its historic extirpation from this region and the possibility that it may happen again. In this perspective, we highlight that paleoecological studies indicate that Russian larch existed not only in alpine regions of Fennoscandia as previously suggested, but also in boreal areas of Sweden, Finland and Latvia. We identified a longitudinal trend where larch populations disappeared from western alpine habitats in Early Holocene but lingered until the last millennia in easter part of Finland. Our empirical analyses of forest experiments suggest that Russian larch has a growth advantage against Scots pine (Pinus sylverstris) and Norway spruce (Picea abies) across contemporary cold Fennoscandian climates, making it unlikely that Russian larch was extirpated simply due to negative growth effects from a colder climate occurring after the Early/Mid Holocene thermal optimum. We highlight that the driver(s) behind the enigmatic extirpation of Russian larch remain unresolved but should warrant attention given the current interest for Russian larch within Fennoscandian forestry.

@article{ko_recruitment_2026,
	title = {Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate},
	volume = {391},
	url = {https://www.science.org/doi/10.1126/science.adx2867},
	doi = {10.1126/science.adx2867},
	abstract = {Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25S ribosomal RNA (rRNA). Residue m3U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.},
	number = {6786},
	urldate = {2026-02-20},
	journal = {Science},
	publisher = {American Association for the Advancement of Science},
	author = {Ko, Donghwi and Ruonala, Raili and Faille, Alexandre and Hellmann, Eva and Help, Hanna and Liu, Huili and Nielsen, Ronni and Haakonsson, Anders and De Diego, Nuria and Paatero, Anja and Shcherbii, Mariia V. and Stefanowicz, Karolina and Ćavar Zeljković, Sanja and Drud Lundager Rasmussen, Tine and Novak, Ondrej and Bodi, Zsuzsanna and Eswaran, Gugan and Wybouw, Brecht and Bourdon, Matthieu and Urbez, Cristina and Liu, Xiaonan and Salokas, Kari and Öhman, Tiina and Waldie, Tanya and Törönen, Petri and el-Showk, Sedeer and Balcerowicz, Martin and Besnard, Fabrice and Liu, Xiaomin and Perkins, Patrick and Mazzoni-Putman, Serina and Vainonen, Julia P. and Sierla, Maija and Frilander, Mikko J. and Mandrup, Susanne and Vernoux, Teva and Ljung, Karin and Ferrando, Alejandro and Blazquez, Miguel A. and Holm, Liisa and Fray, Rupert and Varjosalo, Markku and Leyser, Ottoline and Paavilainen, Ville O. and Mähönen, Ari Pekka and Stepanova, Anna and Alonso, Jose and Heber, Steffen and Malinowski, Robert and Kirpekar, Finn and Warren, Alan J. and Helariutta, Ykä},
	month = feb,
	year = {2026},
	pages = {694--699},
}

Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25S ribosomal RNA (rRNA). Residue m3U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.

@article{ramanathan_effects_2026,
	title = {The {Effects} of {Acorn} {Origin}, {Environmental} {Microbiomes} and {Local} {Adaptation} on the {Leaf} {Metabolome}},
	volume = {52},
	issn = {1573-1561},
	url = {https://doi.org/10.1007/s10886-026-01692-9},
	doi = {10.1007/s10886-026-01692-9},
	abstract = {Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.},
	language = {en},
	number = {1},
	urldate = {2026-02-13},
	journal = {Journal of Chemical Ecology},
	author = {Ramanathan, Chandrasekar and Goris, Lisse and Mishra, Arti and Lihavainen-Bag, Jenna and Pawlowski, Katharina and Albrectsen, Benedicte Riber and Tack, Ayco J.M.},
	month = feb,
	year = {2026},
	keywords = {GC-MS, Local adaptation, Metabolomics, Microbiome, Plant-microbe interactions, Quercus robur},
	pages = {18},
}

Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.

@article{tiziani_deciphering_2026,
	title = {Deciphering underexplored rhizosphere processes: citric acid root acquisition and metabolic journey},
	issn = {0022-0957},
	shorttitle = {Deciphering underexplored rhizosphere processes},
	url = {https://doi.org/10.1093/jxb/erag066},
	doi = {10.1093/jxb/erag066},
	abstract = {Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies. Their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient in hydroponically-grown tomato plants. We applied 13C-labeled citric acid analysed through bulk stable isotope and compound-specific stable isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe content, reduced photosynthesis, altered root morphology and an altered citric acid uptake, which could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake emphasizing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon is allocated to secondary metabolites, while in P deficiency, it supports the TCA and GS-GOGAT cycles. This study is the first to demonstrate citric acid uptake as a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.},
	urldate = {2026-02-13},
	journal = {Journal of Experimental Botany},
	author = {Tiziani, Raphael and Trevisan, Fabio and Hodek, Ondrej and Jämtgård, Sandra and Moritz, Thomas and Bouaicha, Oussama and Chibesa, Mirriam C and Fracasso, Ilaria and Mimmo, Tanja},
	month = feb,
	year = {2026},
	pages = {erag066},
}

Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies. Their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient in hydroponically-grown tomato plants. We applied 13C-labeled citric acid analysed through bulk stable isotope and compound-specific stable isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe content, reduced photosynthesis, altered root morphology and an altered citric acid uptake, which could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake emphasizing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon is allocated to secondary metabolites, while in P deficiency, it supports the TCA and GS-GOGAT cycles. This study is the first to demonstrate citric acid uptake as a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.

@article{liu_photosynthesis-related_2026,
	title = {Photosynthesis-related genetic and transcriptomic variations contribute to adaptive trait diversity in global {Arabidopsis} thaliana populations},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08279-2},
	doi = {10.1186/s12870-026-08279-2},
	abstract = {Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0\% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.},
	language = {en},
	urldate = {2026-02-13},
	journal = {BMC Plant Biology},
	author = {Liu, Wei and Hao, Ruili and Liu, Li and Hou, Jing and Lei, Mengyu and Han, Yu and Zhu, Mingjia and Liang, Lei and Yu, Le and Si, Huan and Liu, Jianquan and Zan, Yanjun and Ji, Yan},
	month = feb,
	year = {2026},
	keywords = {Arabidopsis thaliana, Local adaptation, Natural variation, Photosynthesis pathways},
}

Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.

@article{ma_pangenome_2026,
	title = {A pangenome insight into the genome divergence and flower color diversity among {Rhododendron} species},
	volume = {27},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-025-12461-5},
	doi = {10.1186/s12864-025-12461-5},
	abstract = {The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.},
	language = {en},
	number = {1},
	urldate = {2026-02-13},
	journal = {BMC Genomics},
	author = {Ma, Hai-Yao and Nie, Shuai and Liu, Hai-Bo and Shi, Tian-Le and Zhao, Shi-Wei and Chen, Zhao-Yang and Bao, Yu-Tao and Li, Zhi-Chao and Mao, Jian-Feng},
	month = jan,
	year = {2026},
	keywords = {DNA Transposable Elements, Evolution, Molecular, Flower color, Flowers, Gene duplication, Gene loss, Genetic Variation, Genome, Plant, Genomics, Phylogeny, Pigmentation, Retroelements, Rhododendron, Transposable element},
	pages = {101},
}

The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.

@article{holloway-phillips_rethinking_2026,
	title = {Rethinking the {2H} fingerprint of carbohydrates: a novel proxy for plant metabolism and performance},
	volume = {249},
	issn = {1469-8137},
	shorttitle = {Rethinking the {2H} fingerprint of carbohydrates},
	doi = {10.1111/nph.70845},
	abstract = {The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.},
	language = {eng},
	number = {4},
	journal = {The New Phytologist},
	author = {Holloway-Phillips, Meisha and Lehmann, Marco M. and Tcherkez, Guillaume and Werner, Roland A. and Nelson, Daniel B. and Baan, Jochem and Cernusak, Lucas A. and Cormier, Marc-Andre and Diao, Haoyu and Gessler, Arthur and Guidi, Claudia and Hugger, Selina and Ladd, S. Nemiah and Martínez-Sancho, Elisabet and Niittylä, Totte and Saurer, Matthias and Schuler, Philipp and Vitali, Valentina and Wieloch, Thomas and Kahmen, Ansgar},
	month = feb,
	year = {2026},
	keywords = {Carbohydrate Metabolism, Carbon, Deuterium, Plants, carbohydrates, hydrogen stable isotopes, isotope fractionation, metabolic flux analysis, plant C metabolism, plant physiology},
	pages = {1623--1643},
}

The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.

@article{karamat_arabidopsis_2026,
	title = {Arabidopsis mutants for {Mediator} {Head}, {Middle}, {Tail}, and {Kinase} modules reveal distinct roles in regulating the transcriptional response to salt stress},
	volume = {19},
	issn = {2667-064X},
	url = {https://www.sciencedirect.com/science/article/pii/S2667064X25004567},
	doi = {10.1016/j.stress.2025.101189},
	abstract = {Environmental changes trigger stress responses in living organisms. Although the underlying mechanisms are only partly understood, they involve intricate signaling pathways and transcription factors (TFs). Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. Here, we describe global gene expression changes induced by salt stress in Arabidopsis thaliana. To investigate the involvement of Mediator, we analyzed med9, med16, med18, and cdk8 mutants, each representing one of the four Mediator modules. Our results demonstrate that promoters of differentially expressed genes (DEGs) for each mutant are enriched for binding sites of specific TFs. Phenotypic analyses further support the transcriptomic data: med16 and med18, and to a lesser extent cdk8, exhibit defects typical to mutations that affect abscisic acid and anthocyanin metabolism and we identify dysregulated signaling molecules, TFs, and target genes in these pathways. Our results reveal how signals from different stress response pathways are dependent on, and integrated by, Mediator subunits to coordinate a functional response to salt stress.},
	urldate = {2026-01-23},
	journal = {Plant Stress},
	author = {Karamat, Fazeelat and Vergara, Alexander and Blomberg, Jeanette and Crawford, Tim and Lehotai, Nóra and Rentoft, Matilda and Strand, Åsa and Björklund, Stefan},
	month = jan,
	year = {2026},
	keywords = {Mediator, RNAseq, Salt stress},
	pages = {101189},
}

Environmental changes trigger stress responses in living organisms. Although the underlying mechanisms are only partly understood, they involve intricate signaling pathways and transcription factors (TFs). Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. Here, we describe global gene expression changes induced by salt stress in Arabidopsis thaliana. To investigate the involvement of Mediator, we analyzed med9, med16, med18, and cdk8 mutants, each representing one of the four Mediator modules. Our results demonstrate that promoters of differentially expressed genes (DEGs) for each mutant are enriched for binding sites of specific TFs. Phenotypic analyses further support the transcriptomic data: med16 and med18, and to a lesser extent cdk8, exhibit defects typical to mutations that affect abscisic acid and anthocyanin metabolism and we identify dysregulated signaling molecules, TFs, and target genes in these pathways. Our results reveal how signals from different stress response pathways are dependent on, and integrated by, Mediator subunits to coordinate a functional response to salt stress.

@article{sandehn_bioelectronics_2026,
	title = {Bioelectronics for basic plant science and precision agriculture},
	copyright = {2026 Springer Nature Limited},
	issn = {2948-1201},
	url = {https://www.nature.com/articles/s44287-025-00258-3},
	doi = {10.1038/s44287-025-00258-3},
	abstract = {The rapid growth of the global population and intensified climate challenges make the need for sustainable and efficient food production more urgent than ever. Agriculture is both an important contributor to greenhouse gas emissions and impacted by environmental degradation. Emerging bioelectronic technologies enable real-time monitoring and precise modulation of plant physiology and environmental conditions and have the potential to transform sustainable agriculture. In this Review, we explore the applications of bioelectronics in basic plant science and precision agriculture. In basic research, these technologies can complement or overcome limitations of traditional tools, accelerating efforts to engineer plants that are resistant to environmental stress and have enhanced productivity. In agriculture, bioelectronics offer potential for optimized resource use, enhanced crop yield and early disease detection. While highlighting the interdisciplinary challenges of integrating bioelectronics, from materials and device design through to field deployment and environmental impact, we aim to inform and inspire plant scientists, engineers and agricultural stakeholders.},
	language = {en},
	urldate = {2026-01-23},
	journal = {Nature Reviews Electrical Engineering},
	publisher = {Nature Publishing Group},
	author = {Sandéhn, Alexandra and Vijayarouthu, S. S. V. Prasanna and Costa, Alex and Stavrinidou, Eleni},
	month = jan,
	year = {2026},
	keywords = {Biological techniques, Electrical and electronic engineering, Sensors and biosensors},
	pages = {1--12},
}

The rapid growth of the global population and intensified climate challenges make the need for sustainable and efficient food production more urgent than ever. Agriculture is both an important contributor to greenhouse gas emissions and impacted by environmental degradation. Emerging bioelectronic technologies enable real-time monitoring and precise modulation of plant physiology and environmental conditions and have the potential to transform sustainable agriculture. In this Review, we explore the applications of bioelectronics in basic plant science and precision agriculture. In basic research, these technologies can complement or overcome limitations of traditional tools, accelerating efforts to engineer plants that are resistant to environmental stress and have enhanced productivity. In agriculture, bioelectronics offer potential for optimized resource use, enhanced crop yield and early disease detection. While highlighting the interdisciplinary challenges of integrating bioelectronics, from materials and device design through to field deployment and environmental impact, we aim to inform and inspire plant scientists, engineers and agricultural stakeholders.

@article{bekele_associations_2026,
	title = {Associations between volatile fatty acid profiles, methane emissions, and rumen microbiota in sheep fed {Ethiopian} forage},
	volume = {16},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1731623/full},
	doi = {10.3389/fmicb.2025.1731623},
	abstract = {This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD\_0), 45 (SD\_45), and 90 (SD\_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9\% of ASVs were Bacteria, and 0.05\% Archaea. At the genus level, Rikenellaceae RC9 gut group (18\%), Prevotella (17\%), and Candidatus Saccharimonas (8.9\%) were the most abundant Bacteria, while Methanobrevibacter (88\%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.},
	language = {English},
	urldate = {2026-01-23},
	journal = {Frontiers in Microbiology},
	publisher = {Frontiers},
	author = {Bekele, Wondimagegne and Mahawar, Lovely and Ramin, Mohammad and Simachew, Addis and Albrectsen, Benedicte Riber and Zegeye, Abiy},
	month = jan,
	year = {2026},
	keywords = {Archaea, Bacteria, CH4 intensity, Illumina sequencing, gut microbiota, metabarcoding, ruminant, volatile fatty acids},
}

This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD_0), 45 (SD_45), and 90 (SD_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9% of ASVs were Bacteria, and 0.05% Archaea. At the genus level, Rikenellaceae RC9 gut group (18%), Prevotella (17%), and Candidatus Saccharimonas (8.9%) were the most abundant Bacteria, while Methanobrevibacter (88%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.

@article{pandey_variable_2026,
	title = {Variable temperature processing by plasmodesmata regulates robust bud dormancy release},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-67260-z},
	doi = {10.1038/s41467-025-67260-z},
	abstract = {Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.},
	language = {en},
	number = {1},
	urldate = {2026-01-16},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Pandey, Shashank K. and Moraes, Tatiana S. and Nair, Aswin and Aryal, Bibek and Azeez, Abdul and Miskolczi, Pal and Maucort, Guillaume and Cordelières, Fabrice P. and Brocard, Lysiane and Davis, Gwendolyn V. and Dromiack, Hannah and Khanapurkar, Swanand and Walker, Sara I. and Bassel, George W. and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2026},
	keywords = {Plant molecular biology, Plant physiology, Shoot apical meristem},
	pages = {348},
}

Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.

@article{parizkova_l-glutamine_2026,
	title = {L-{Glutamine} {Modulates} {Root} {Architecture} and {Hormonal} {Balance} in {Arabidopsis}},
	volume = {178},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70723},
	doi = {10.1111/ppl.70723},
	abstract = {Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Physiologia Plantarum},
	author = {Pařízková, Barbora and Johansson, Annika I. and Juvany, Marta and Šimura, Jan and Ljung, Karin and Antoniadi, Ioanna},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70723},
	keywords = {KNO3, L-GLN, auxin, cytokinin, organic N, root growth, root system architecture},
	pages = {e70723},
}

Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.

@article{marciano_comparative_2026,
	title = {A {Comparative} {Analysis} of {Receptor}-{Like} {Kinases} in {Chlorophyta} {Reveals} the {Presence} of {Putative} {Cell} {Wall} {Integrity} {Sensors}},
	volume = {178},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70703},
	doi = {10.1111/ppl.70703},
	abstract = {Receptor-like kinases (RLKs) detect external and internal signals, triggering responses essential for growth and adaptation. Among internal cues, cell wall integrity (CWI) sensing plays a key role, as changes in cell wall structure activate responses critical for development and defense. While RLKs are well-studied in vascular plants, their diversity and function remain largely unknown in green algae belonging to the Chlorophyta phylum, a group that is relevant for global oxygen production and carbon cycling. Due to their varied cell wall structures, Chlorophyta offer a useful system to study the origins of CWI sensing. In this study, we used advanced bioinformatics and AI-based tools to analyze RLKs in 34 Chlorophyta species, mapping their distribution, structural features, and similarity to plant RLKs. We identified 736 putative RLKs, expanding the known repertoire in green algae. Structural analyses showed a wide range of extracellular domains, including motifs related to plant CWI sensors: domains mediating protein interactions (e.g., Leucine Rich Repeats—LRR, Plasminogen Apple Nematod e-PAN, Armadillo repeat—ARM), cell wall remodeling (e.g., glycosyl hydrolases, lyases), and mechanosensing (e.g., Leucine-Proline-X-Threonine-Glycine motifs—LPXTG, Fibronectin). This diversity suggests that mechanisms for extracellular sensing and CWI monitoring emerged early in evolution. The results provide a basis for future studies on the function of RLKs in algae and their evolutionary links to vascular plant signaling.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Physiologia Plantarum},
	author = {Marcianò, Demetrio and Dauphin, Bastien G. and Basso, Fabian and Funk, Christiane and Bacete, Laura},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70703},
	keywords = {Chlorella vulgaris, algae-plants evolutionary conservation, microalgae signal transduction, receptor functional divergence},
	pages = {e70703},
}

Receptor-like kinases (RLKs) detect external and internal signals, triggering responses essential for growth and adaptation. Among internal cues, cell wall integrity (CWI) sensing plays a key role, as changes in cell wall structure activate responses critical for development and defense. While RLKs are well-studied in vascular plants, their diversity and function remain largely unknown in green algae belonging to the Chlorophyta phylum, a group that is relevant for global oxygen production and carbon cycling. Due to their varied cell wall structures, Chlorophyta offer a useful system to study the origins of CWI sensing. In this study, we used advanced bioinformatics and AI-based tools to analyze RLKs in 34 Chlorophyta species, mapping their distribution, structural features, and similarity to plant RLKs. We identified 736 putative RLKs, expanding the known repertoire in green algae. Structural analyses showed a wide range of extracellular domains, including motifs related to plant CWI sensors: domains mediating protein interactions (e.g., Leucine Rich Repeats—LRR, Plasminogen Apple Nematod e-PAN, Armadillo repeat—ARM), cell wall remodeling (e.g., glycosyl hydrolases, lyases), and mechanosensing (e.g., Leucine-Proline-X-Threonine-Glycine motifs—LPXTG, Fibronectin). This diversity suggests that mechanisms for extracellular sensing and CWI monitoring emerged early in evolution. The results provide a basis for future studies on the function of RLKs in algae and their evolutionary links to vascular plant signaling.

@article{chanwala_functions_2026,
	title = {The functions of long noncoding {RNAs} in plants},
	volume = {89},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S136952662500144X},
	doi = {10.1016/j.pbi.2025.102830},
	abstract = {Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.},
	urldate = {2025-12-18},
	journal = {Current Opinion in Plant Biology},
	author = {Chanwala, Jeky and Rosenkranz, Isabell and Kindgren, Peter},
	month = feb,
	year = {2026},
	pages = {102830},
}

Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.

@article{vergara_isoformmapper_2026,
	title = {{IsoformMapper}: a web application for protein-level comparison of splice variants through structural community analysis},
	volume = {32},
	issn = {1355-8382, 1469-9001},
	shorttitle = {{IsoformMapper}},
	url = {http://rnajournal.cshlp.org/content/32/1/1},
	doi = {10.1261/rna.080738.125},
	abstract = {Alternative splicing (AS) enables cells to produce multiple protein isoforms from single genes, fine-tuning protein function across numerous cellular processes. However, despite its biological importance, researchers lack effective tools to compare the domain composition of AS-derived protein isoforms because such comparisons require both structural data and specialized methods. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, now make accurate structural determination of splicing isoforms accessible, enabling functional AS analysis at the protein structure level. Here, we present IsoformMapper, a web resource that analyzes AS through network community analysis of protein structures. This approach captures 3D physical interactions between protein regions often missed by traditional domain analysis, enabling structural comparisons of isoforms across any biological system. We illustrate our tool by analyzing validated human Bcl-X protein isoforms, revealing how AS creates distinct community structures with antagonistic functional roles. As a proof of concept, we apply our tool to investigate how GENOMES UNCOUPLED1 (GUN1)–dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, gun1 shows alterations in spliceosome component expression, suggesting that GUN1 contributes to AS regulation of genes essential for photosynthetic establishment. The gun1 mutant displays altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool reveals that these isoforms form distinct protein community structures, demonstrating how AS impacts protein function and validating IsoformMapper's practical value.},
	language = {en},
	number = {1},
	urldate = {2025-12-18},
	journal = {RNA},
	publisher = {Cold Spring Harbor Lab},
	author = {Vergara, Alexander and Hernández-Verdeja, Tamara and Ojeda-May, Pedro and Ramirez, Leonor and Edler, Daniel and Rosvall, Martin and Strand, Åsa},
	month = jan,
	year = {2026},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press},
	keywords = {alternative splicing, plastid retrograde signaling},
	pages = {1--20},
}

Alternative splicing (AS) enables cells to produce multiple protein isoforms from single genes, fine-tuning protein function across numerous cellular processes. However, despite its biological importance, researchers lack effective tools to compare the domain composition of AS-derived protein isoforms because such comparisons require both structural data and specialized methods. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, now make accurate structural determination of splicing isoforms accessible, enabling functional AS analysis at the protein structure level. Here, we present IsoformMapper, a web resource that analyzes AS through network community analysis of protein structures. This approach captures 3D physical interactions between protein regions often missed by traditional domain analysis, enabling structural comparisons of isoforms across any biological system. We illustrate our tool by analyzing validated human Bcl-X protein isoforms, revealing how AS creates distinct community structures with antagonistic functional roles. As a proof of concept, we apply our tool to investigate how GENOMES UNCOUPLED1 (GUN1)–dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, gun1 shows alterations in spliceosome component expression, suggesting that GUN1 contributes to AS regulation of genes essential for photosynthetic establishment. The gun1 mutant displays altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool reveals that these isoforms form distinct protein community structures, demonstrating how AS impacts protein function and validating IsoformMapper's practical value.

@article{skalicky_illuminating_2026,
	title = {Illuminating the subcellular maze: fluorescence-activated organelle sorting in plant sciences},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {Illuminating the subcellular maze},
	url = {https://doi.org/10.1093/jxb/eraf490},
	doi = {10.1093/jxb/eraf490},
	abstract = {The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ, and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence-activated organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.},
	number = {1},
	urldate = {2025-12-18},
	journal = {Journal of Experimental Botany},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Ljung, Karin and Novák, Ondřej},
	month = jan,
	year = {2026},
	pages = {120--133},
}

The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ, and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence-activated organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.

@incollection{shankar_microproteins_2026,
	address = {New York, NY},
	title = {Microproteins: {Uncovering} {Hidden} {Layers} of the {Proteome}},
	isbn = {978-1-0716-5013-4},
	shorttitle = {Microproteins},
	url = {https://doi.org/10.1007/978-1-0716-5013-4_1},
	doi = {10.1007/978-1-0716-5013-4_1},
	abstract = {Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.},
	language = {en},
	urldate = {2025-11-21},
	booktitle = {Microproteins: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Shankar, Naveen and Wenkel, Stephan},
	editor = {Wenkel, Stephan},
	year = {2026},
	keywords = {Evolution, Microproteins, Protein structure, lncRNAs, sORFs},
	pages = {3--18},
}

Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.

@article{munoz_lysine_2026,
	title = {Lysine potentiates insulin secretion via {AASS}-dependent catabolism and regulation of {GABA} content and signaling},
	volume = {174},
	issn = {0026-0495},
	url = {https://www.sciencedirect.com/science/article/pii/S0026049525002926},
	doi = {10.1016/j.metabol.2025.156423},
	abstract = {Lysine is an essential amino acid with insulinotropic effects in humans. In vitro, it enhances glucose-stimulated insulin secretion (GSIS) in β-cell lines and rodent islets. While lysine is thought to act via membrane depolarization similar to arginine, the role of its intracellular metabolism in β-cell function remains unexplored. Here, we show that lysine acutely potentiates GSIS and that genes encoding enzymes in the lysine degradation pathway, including AminoAdipate-Semialdehyde Synthase (AASS), a key mitochondrial enzyme catalysing the first two steps of lysine catabolism, were present in human pancreatic islets and INS1 832/13 β cells. Some of these genes including AASS, ALDH7A1, DHTKD1, and HADH, were downregulated in pancreatic islets from type 2 diabetes (T2D) versus non-diabetic (ND) donors. Silencing AASS in human islets and INS1 832/13 β cells led to reduced GSIS. Integrated transcriptomics and metabolomics revealed altered expression of GABA metabolism genes, reduced GABA content and accumulation of glutamate in Aass-KD cells. Mitochondrial TCA cycle and OXPHOS function was impaired, evidenced by decreased ATP/ADP ratio, diminished glucose-stimulated mitochondrial respiration, and elevated lactate/pyruvate ratio. Cytosolic calcium responses to glucose and GABA were also disrupted. Pharmacological analyses demonstrated that inhibition of GABA synthesis or degradation did not account for the reduced GSIS, but providing substrates and activation of GDH partially restored insulin secretion, pointing to a diminished glutamate supply as a contributing factor. Remarkably, exogenous GABA restored insulin secretion in β cells and human islets with suppressed AASS-dependent lysine catabolism, supporting a role for GABA as both a metabolic substrate and signaling effector. Together, these findings identify AASS-mediated lysine catabolism as a critical regulator of β-cell metabolic integrity, linking impaired lysine metabolism to GABA depletion, mitochondrial dysfunction, and secretory failure in T2D islets. They also underscore the nutritional importance of essential amino acids such as lysine in sustaining GSIS and glucose homeostasis, and support therapeutic strategies aimed at restoring lysine catabolism or GABA/glutamate balance to maintain β-cell function.},
	urldate = {2025-11-07},
	journal = {Metabolism},
	author = {Muñoz, Felipe and Gao, Qian and Mattanovich, Matthias and Trost, Kajetan and Hodek, Ondřej and Lindqvist, Andreas and Wierup, Nils and Fex, Malin and Moritz, Thomas and Mulder, Hindrik and Cataldo, Luis Rodrigo},
	month = jan,
	year = {2026},
	keywords = {AASS, Amino acids, GABA, GABA shunt, GDH, Glutamate, Insulin secretion, Lysine, Mitochondrial metabolism, TCA cycle, Type 2 diabetes},
	pages = {156423},
}

Lysine is an essential amino acid with insulinotropic effects in humans. In vitro, it enhances glucose-stimulated insulin secretion (GSIS) in β-cell lines and rodent islets. While lysine is thought to act via membrane depolarization similar to arginine, the role of its intracellular metabolism in β-cell function remains unexplored. Here, we show that lysine acutely potentiates GSIS and that genes encoding enzymes in the lysine degradation pathway, including AminoAdipate-Semialdehyde Synthase (AASS), a key mitochondrial enzyme catalysing the first two steps of lysine catabolism, were present in human pancreatic islets and INS1 832/13 β cells. Some of these genes including AASS, ALDH7A1, DHTKD1, and HADH, were downregulated in pancreatic islets from type 2 diabetes (T2D) versus non-diabetic (ND) donors. Silencing AASS in human islets and INS1 832/13 β cells led to reduced GSIS. Integrated transcriptomics and metabolomics revealed altered expression of GABA metabolism genes, reduced GABA content and accumulation of glutamate in Aass-KD cells. Mitochondrial TCA cycle and OXPHOS function was impaired, evidenced by decreased ATP/ADP ratio, diminished glucose-stimulated mitochondrial respiration, and elevated lactate/pyruvate ratio. Cytosolic calcium responses to glucose and GABA were also disrupted. Pharmacological analyses demonstrated that inhibition of GABA synthesis or degradation did not account for the reduced GSIS, but providing substrates and activation of GDH partially restored insulin secretion, pointing to a diminished glutamate supply as a contributing factor. Remarkably, exogenous GABA restored insulin secretion in β cells and human islets with suppressed AASS-dependent lysine catabolism, supporting a role for GABA as both a metabolic substrate and signaling effector. Together, these findings identify AASS-mediated lysine catabolism as a critical regulator of β-cell metabolic integrity, linking impaired lysine metabolism to GABA depletion, mitochondrial dysfunction, and secretory failure in T2D islets. They also underscore the nutritional importance of essential amino acids such as lysine in sustaining GSIS and glucose homeostasis, and support therapeutic strategies aimed at restoring lysine catabolism or GABA/glutamate balance to maintain β-cell function.