@article{liu_uncovering_2026,
	title = {Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges},
	issn = {1537-1719},
	shorttitle = {Uncovering structural variation in conifer gigagenomes},
	url = {https://doi.org/10.1093/molbev/msag239},
	doi = {10.1093/molbev/msag239},
	abstract = {Structural variants (SVs) are a major yet understudied source of genomic variation in conifers, whose large, repeat-rich genomes have hindered systematic SV discovery. Here, we combined whole-genome long-read and short-read sequencing to characterize the genomic landscape, functional impact, and evolutionary significance of SVs in a complex of three closely related pine species (Pinus densata, P. tabuliformis, and P. yunnanensis) with a hybridization history. From 21 long-read-sequenced individuals, we identified 5.7 million SVs, comprising 52\% insertions, 43\% deletions, and 5\% inversions, duplications, and translocations. Approximately 97\% of SVs were located in intergenic and intronic regions, and 60\% overlapped transposable elements, whose activity shapes SV abundance and size variation. The proportion of loss-of-function (LoF) mutations was hundreds-fold higher among SVs than SNPs, with longer SVs more likely to cause LoF effects across all SV classes. Estimates of population diversity based on SVs and SNPs were largely concordant. In P. densata, the retention of parental SVs highlights the genomic signature of its admixed ancestry. We conducted graph pangenome-based SV genotyping in 29 short-read-sequenced individuals, yielding 44\% recall and 70\% precision, underlining the challenge of accurately recovering long-read-derived SVs in highly repetitive conifer genomes. Population-level selection scans on SNPs and genotyped SVs identified only 19\% of candidate gene loci in common, indicating that the two marker types capture complementary components of environmental adaptation. Our findings demonstrate the importance of SVs as a dimension of genomic diversity and provide a foundation for integrating structural variation into evolutionary studies, conservation genomics, and tree breeding.},
	urldate = {2026-10-02},
	journal = {Molecular Biology and Evolution},
	author = {Liu, Hui and Zhao, Wei and Guo, Jing-Fang and Yan, Xue-Mei and Liu, Yan-Jing and Zeng, Qing-Yin and Wang, Xiao-Ru},
	month = sep,
	year = {2026},
	pages = {msag239},
}

Structural variants (SVs) are a major yet understudied source of genomic variation in conifers, whose large, repeat-rich genomes have hindered systematic SV discovery. Here, we combined whole-genome long-read and short-read sequencing to characterize the genomic landscape, functional impact, and evolutionary significance of SVs in a complex of three closely related pine species (Pinus densata, P. tabuliformis, and P. yunnanensis) with a hybridization history. From 21 long-read-sequenced individuals, we identified 5.7 million SVs, comprising 52% insertions, 43% deletions, and 5% inversions, duplications, and translocations. Approximately 97% of SVs were located in intergenic and intronic regions, and 60% overlapped transposable elements, whose activity shapes SV abundance and size variation. The proportion of loss-of-function (LoF) mutations was hundreds-fold higher among SVs than SNPs, with longer SVs more likely to cause LoF effects across all SV classes. Estimates of population diversity based on SVs and SNPs were largely concordant. In P. densata, the retention of parental SVs highlights the genomic signature of its admixed ancestry. We conducted graph pangenome-based SV genotyping in 29 short-read-sequenced individuals, yielding 44% recall and 70% precision, underlining the challenge of accurately recovering long-read-derived SVs in highly repetitive conifer genomes. Population-level selection scans on SNPs and genotyped SVs identified only 19% of candidate gene loci in common, indicating that the two marker types capture complementary components of environmental adaptation. Our findings demonstrate the importance of SVs as a dimension of genomic diversity and provide a foundation for integrating structural variation into evolutionary studies, conservation genomics, and tree breeding.

@article{choudhary_nitrate_2026,
	title = {Nitrate transiently rewires transcription in developing xylem of {Populus} wood to promote cell expansion via {CRF4}},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koag281},
	doi = {10.1093/plcell/koag281},
	abstract = {Nitrate functions both as a nutrient and a signaling molecule, but how nitrate is perceived and translated into developmental outputs within woody tissues is unknown. Here, we show that developing xylem in hybrid aspen (Populus tremula × P. tremuloides) mounts a rapid, cell-type-specific transcriptional response to nitrate that promotes xylem cell expansion. To isolate local nitrate signaling in wood-forming tissues, we delivered nitrate directly into the xylem sap and profiled transcriptomic responses from 2 to 48 h after treatment. Bulk RNA sequencing revealed a transient response peaking within 2–4 h. Single-cell RNA sequencing at the peak response resolved nitrate signaling across developing xylem cell types and showed that nitrate induced cell-type-specific programs linked to nitrogen transport, cell wall remodeling, and developmental progression, while repressing lignin-biosynthetic genes. These data indicate that nitrate acts transiently in wood-forming tissues to fine-tune early xylem development. Among nitrate-responsive transcription factors, CYTOKININ RESPONSE FACTOR 4 (CRF4) emerged as a candidate regulator of this response. CRF4 overexpression in hybrid aspen stimulated xylem cell expansion, whereas simultaneous knock-out of CRF4 and its paralog, CRF3, significantly attenuated the nitrate-induced expansion. Together, our findings identify a local nitrate signaling module in developing wood and establish CRF4 as a component linking nitrate sensing to xylem cell expansion.},
	urldate = {2026-10-02},
	journal = {The Plant Cell},
	author = {Choudhary, Shruti and Renström, Anna and Kochakarn, Theerarat Fai and Miskolczi, Pal and Piombo, Edoardo and Chantreau, Maxime and Jose, Jeny and Jämtgård, Sandra and Gorzsás, András and Henriksson, Johan and Tuominen, Hannele},
	month = sep,
	year = {2026},
	pages = {koag281},
}

Nitrate functions both as a nutrient and a signaling molecule, but how nitrate is perceived and translated into developmental outputs within woody tissues is unknown. Here, we show that developing xylem in hybrid aspen (Populus tremula × P. tremuloides) mounts a rapid, cell-type-specific transcriptional response to nitrate that promotes xylem cell expansion. To isolate local nitrate signaling in wood-forming tissues, we delivered nitrate directly into the xylem sap and profiled transcriptomic responses from 2 to 48 h after treatment. Bulk RNA sequencing revealed a transient response peaking within 2–4 h. Single-cell RNA sequencing at the peak response resolved nitrate signaling across developing xylem cell types and showed that nitrate induced cell-type-specific programs linked to nitrogen transport, cell wall remodeling, and developmental progression, while repressing lignin-biosynthetic genes. These data indicate that nitrate acts transiently in wood-forming tissues to fine-tune early xylem development. Among nitrate-responsive transcription factors, CYTOKININ RESPONSE FACTOR 4 (CRF4) emerged as a candidate regulator of this response. CRF4 overexpression in hybrid aspen stimulated xylem cell expansion, whereas simultaneous knock-out of CRF4 and its paralog, CRF3, significantly attenuated the nitrate-induced expansion. Together, our findings identify a local nitrate signaling module in developing wood and establish CRF4 as a component linking nitrate sensing to xylem cell expansion.

@article{chakravarty_investigating_2026,
	title = {Investigating bioremediation of micro- and nanoplastics by a {Nordic} polyculture isolated from wastewater},
	issn = {2213-3437},
	url = {https://www.sciencedirect.com/science/article/pii/S2213343726040662},
	doi = {10.1016/j.jece.2026.125091},
	abstract = {The potential toxicity of micro- and nanoplastics (MNPs) highlights an urgent need for effective and sustainable bioremediation strategies. This study provides an in-depth investigation of the interaction and bioremediation of MNPs by a natural Nordic microalgal polyculture isolated from an open raceway pond reactor treating municipal wastewater. Reduced but uniform growth, photosynthetic yield and pigment composition was observed in the microalgae when the polyculture was exposed to nanoplastics consisting of polystyrene (PS), polymethyl methacrylate (PMMA) and microplastics of polyvinyl chloride (PVC) at concentrations of 25, 50 or 100 ppm for 8 days. The total carbohydrate-, lipid-, and EPS-contents were recorded to be ⁓8–30\% higher under MNP-exposure, suggesting the generation of moderate but manageable oxidative stress. Moderately elevated levels of lipid peroxidation and enhanced activity of the antioxidant enzymes catalase and ascorbate peroxidase revealed an effective defence response of the polyculture. Among the three MNPs, PMMA was noted to induce highest oxidative stress resulting in starch accretion as storage carbon. Electron microscopy revealed attachment of the MNPs to the microalgal cell surface, forming hetero-aggregates. Infrared spectroscopy confirmed these results by detecting MNP-specific functional groups in the biomass. Analysis of MNP concentrations in the media after polyculture treatment showed removal efficiencies of approximately 78–90\% at initial MNP concentrations of 100 ppm and 50–60\% at initial concentrations of 25 and 50 ppm. Therefore, this study provides valuable insights and strong environmental relevance in exploring microalgae-based pathways for the bioremediation of the increasingly widespread MNP pollution.},
	urldate = {2026-10-02},
	journal = {Journal of Environmental Chemical Engineering},
	author = {Chakravarty, Saumita and Takahashi, Junko and Funk, Christiane},
	month = sep,
	year = {2026},
	keywords = {Defence response, Hetero-aggregation, Micro- and nanoplastics, Nordic polyculture, Removal efficiency, Wastewater},
	pages = {125091},
}

The potential toxicity of micro- and nanoplastics (MNPs) highlights an urgent need for effective and sustainable bioremediation strategies. This study provides an in-depth investigation of the interaction and bioremediation of MNPs by a natural Nordic microalgal polyculture isolated from an open raceway pond reactor treating municipal wastewater. Reduced but uniform growth, photosynthetic yield and pigment composition was observed in the microalgae when the polyculture was exposed to nanoplastics consisting of polystyrene (PS), polymethyl methacrylate (PMMA) and microplastics of polyvinyl chloride (PVC) at concentrations of 25, 50 or 100 ppm for 8 days. The total carbohydrate-, lipid-, and EPS-contents were recorded to be ⁓8–30% higher under MNP-exposure, suggesting the generation of moderate but manageable oxidative stress. Moderately elevated levels of lipid peroxidation and enhanced activity of the antioxidant enzymes catalase and ascorbate peroxidase revealed an effective defence response of the polyculture. Among the three MNPs, PMMA was noted to induce highest oxidative stress resulting in starch accretion as storage carbon. Electron microscopy revealed attachment of the MNPs to the microalgal cell surface, forming hetero-aggregates. Infrared spectroscopy confirmed these results by detecting MNP-specific functional groups in the biomass. Analysis of MNP concentrations in the media after polyculture treatment showed removal efficiencies of approximately 78–90% at initial MNP concentrations of 100 ppm and 50–60% at initial concentrations of 25 and 50 ppm. Therefore, this study provides valuable insights and strong environmental relevance in exploring microalgae-based pathways for the bioremediation of the increasingly widespread MNP pollution.

@article{goretti_methylosome_2026,
	title = {Methylosome and survival motor neuron complexes are dispensable for plant viability in {Arabidopsis} thaliana},
	volume = {202},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiag667},
	doi = {10.1093/plphys/kiag667},
	abstract = {The role of RNA splicing as a modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures has only recently started to emerge. Here, we analyzed the role of temperature in regulating the functionality of factors associated with small nuclear ribonucleoprotein (snRNP) biogenesis, a key process underlying pre-mRNA splicing. Taking advantage of mutants showing temperature-dependent phenotypes, we conducted a comprehensive study of the role that the methylosome and survival motor neuron (SMN) complexes have in plant development. Genetic, phylogenetic, and confocal analyses, as well as in vivo and in vitro evidence, reveal remarkable differences in the composition and importance of these complexes between plants and vertebrate animals. The SMN complex in Arabidopsis is apparently reduced to a single protein, GEMIN2, that is not essential for plant development, and the existence of an SMN ortholog is uncertain. Similarly, components of the methylosome previously implicated in snRNP biogenesis are not essential for plant viability. Our results suggest that factors considered central to snRNP biogenesis in animals have less crucial roles in plants and highlight how an evolutionarily conserved molecular process like RNA splicing has nevertheless evolved plant-specific characteristics.},
	number = {1},
	urldate = {2026-10-02},
	journal = {Plant Physiology},
	author = {Goretti, Daniela and Collani, Silvio and Nardeli, Sarah Muniz and Ratnakaram, Hemamshu and Robert, Stéphanie and Schmid, Markus},
	month = sep,
	year = {2026},
	pages = {kiag667},
}

The role of RNA splicing as a modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures has only recently started to emerge. Here, we analyzed the role of temperature in regulating the functionality of factors associated with small nuclear ribonucleoprotein (snRNP) biogenesis, a key process underlying pre-mRNA splicing. Taking advantage of mutants showing temperature-dependent phenotypes, we conducted a comprehensive study of the role that the methylosome and survival motor neuron (SMN) complexes have in plant development. Genetic, phylogenetic, and confocal analyses, as well as in vivo and in vitro evidence, reveal remarkable differences in the composition and importance of these complexes between plants and vertebrate animals. The SMN complex in Arabidopsis is apparently reduced to a single protein, GEMIN2, that is not essential for plant development, and the existence of an SMN ortholog is uncertain. Similarly, components of the methylosome previously implicated in snRNP biogenesis are not essential for plant viability. Our results suggest that factors considered central to snRNP biogenesis in animals have less crucial roles in plants and highlight how an evolutionarily conserved molecular process like RNA splicing has nevertheless evolved plant-specific characteristics.

@article{postel_evolutionary_2026,
	title = {Evolutionary consequences of repeated loss of distyly in {Linum}},
	journal = {Genome Biology and Evolution},
	author = {Postel, Zoé and Zervakis, Panagiotis-Ioannis and Fracassetti, Marco and Losvik, Aleksandra and Wanntorp, Matias and Soler, Lucile and Churcher, Allison and Humphreys, Aelys M and Slotte, Tanja},
	year = {2026},
}