@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{liu_glycoalkaloid-free_2025,
	title = {Glycoalkaloid-{Free} {Starch} {Potatoes} {Generated} by {CRISPR}/{Cas9}-{Mediated} {Mutations} of {Genes} in the {Glycoalkaloid} {Biosynthesis} {Pathway} {Enable} {More} {Sustainable} {Uses} of {By}-{Products} {From} {Starch} {Production}},
	copyright = {© 2025 Sweden's Starch Producers Association and The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70412},
	doi = {10.1111/pbi.70412},
	abstract = {Steroidal glycoalkaloids (SGAs) are toxic cholesterol-derived secondary metabolites present in several Solanaceae species. In potato, tuber SGA levels are for reasons of toxicity of concern in both table and starch cultivars. In the latter, SGAs bind to proteins and fibres in starch production side-streams and prevent their further uses as food and feed. To enable more sustainable uses of starch by-products, we have here reduced SGA biosynthesis in a starch potato cultivar using DNA-free CRISPR/Cas9. Six SGA genes were targeted, encoding enzymes acting either before cholesterol (SMO1-L, DWF1-L, DWF7-L), or after (16DOX, CYP88B1, TAMiso2). Editing efficiencies varied between 20\% and 49\%, and generated mutants were investigated under greenhouse and field conditions. Target mass-spectrometric analyses confirmed reduced SGA levels and alterations of sterol metabolism in mutated events. Plant height and tuber yield were reduced in several events, although this was not correlated to low SGA levels. Several knockout mutants had almost SGA-free leaves and tubers, the latter also under two SGA-inducing conditions. Similarly, both fibre and protein fractions isolated from side-streams in the starch production process from mutant tubers had very low SGA levels. By contrast, the corresponding wild-type SGA levels were almost 10-fold and, respectively, 40-fold higher than the recommended upper safe limit. The results demonstrate that glycoalkaloid-free mutants can be generated and grown with moderate yield reductions under both greenhouse and field conditions. This suggests a potential for sustainable production of high-value products, e.g., food-grade protein and fibre, from starch production side-streams of SGA knockout tubers.},
	language = {en},
	urldate = {2025-10-24},
	journal = {Plant Biotechnology Journal},
	author = {Liu, Ying and Merino, Irene and Gutensohn, Mareike and Johansson, Annika I. and Johansson, Kalle and Andersson, Mariette and Hofvander, Per and Sitbon, Folke},
	month = oct,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70412},
	keywords = {CRISPR/Cas9, potato (Solanum tuberosum), potato protein, starch potatoes, steroidal glycoalkaloids, sustainable food production},
}

Steroidal glycoalkaloids (SGAs) are toxic cholesterol-derived secondary metabolites present in several Solanaceae species. In potato, tuber SGA levels are for reasons of toxicity of concern in both table and starch cultivars. In the latter, SGAs bind to proteins and fibres in starch production side-streams and prevent their further uses as food and feed. To enable more sustainable uses of starch by-products, we have here reduced SGA biosynthesis in a starch potato cultivar using DNA-free CRISPR/Cas9. Six SGA genes were targeted, encoding enzymes acting either before cholesterol (SMO1-L, DWF1-L, DWF7-L), or after (16DOX, CYP88B1, TAMiso2). Editing efficiencies varied between 20% and 49%, and generated mutants were investigated under greenhouse and field conditions. Target mass-spectrometric analyses confirmed reduced SGA levels and alterations of sterol metabolism in mutated events. Plant height and tuber yield were reduced in several events, although this was not correlated to low SGA levels. Several knockout mutants had almost SGA-free leaves and tubers, the latter also under two SGA-inducing conditions. Similarly, both fibre and protein fractions isolated from side-streams in the starch production process from mutant tubers had very low SGA levels. By contrast, the corresponding wild-type SGA levels were almost 10-fold and, respectively, 40-fold higher than the recommended upper safe limit. The results demonstrate that glycoalkaloid-free mutants can be generated and grown with moderate yield reductions under both greenhouse and field conditions. This suggests a potential for sustainable production of high-value products, e.g., food-grade protein and fibre, from starch production side-streams of SGA knockout tubers.

@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.