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<title>bioRxiv Subject Collection: Genetics Plant Biology</title>
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This feed contains articles for bioRxiv Subject Collection "Genetics Plant Biology"
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.23.720446v1?rss=1">
<title>
<![CDATA[
Linked origins but distinct roles for extreme length and sequence variation at a tandem repeat in CACNA1C 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.23.720446v1?rss=1
</link>
<description><![CDATA[
Length variation in tandem repeats is a well-established driver of disease risk and is commonly assumed to arise from persistent genomic instability. Here, we characterize TRACT, a 30-bp variable number tandem repeat (VNTR) intronic to the calcium channel gene CACNA1C. TRACT exhibits extreme length variation (3-30+ kb) and has been previously linked to risk for bipolar disorder and schizophrenia. By examining multiple human cohorts, we find that TRACT alleles are strikingly bimodal in both length and sequence composition. Short alleles (TRACTS, ~6 kb) and long alleles (TRACTL, ~24 kb) are enriched for distinct 30-bp variants and are found on separate haplotypes that arose prior to the human migration out of Africa. Our data suggest that these ancient alleles expanded via perfect repeat tracts that were disrupted by accumulated mutations to result in relative length stability in extant humans, where there is no evidence for overt germline or somatic instability. Interestingly, neuropsychiatric disease risk is associated with specific 30-bp variants within TRACTS alleles, but not with overall TRACT length or with 30-bp variants enriched in TRACTL alleles. Instead, TRACTL alleles are associated with decreased gene expression in fibroblasts and testis. Together, these findings motivate joint examination of both sequence composition and length variation to fully understand the effects of VNTRs on evolution, trait variation, and disease risk.
]]></description>
<dc:creator><![CDATA[ Song, J., Zhao, V., Grant, R. L., Kingsley, D. M. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.23.720446</dc:identifier>
<dc:title><![CDATA[Linked origins but distinct roles for extreme length and sequence variation at a tandem repeat in CACNA1C]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719884v1?rss=1">
<title>
<![CDATA[
Is constitutive red-shift an advantage for oxygenic photosynthesis under M-dwarf starlight? Insights from Acaryochloris marina sp. str. Moss Beach 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719884v1?rss=1
</link>
<description><![CDATA[
In the next years, several space missions will search for evidence of life on exoplanets, focusing on robust biosignatures associated with oxygenic photosynthesis, including atmospheric oxygen accumulation and the Vegetation Red-Edge in surface reflectance spectra. Many potentially habitable rocky exoplanets orbit M-dwarf stars, whose spectral energy distribution may challenge oxygenic photosynthesis. Differently from the Sun, M-dwarf stars emit predominantly far-red (700-750 nm) and infrared (750-1000 nm) light, and relatively little visible (400-700 nm) radiation, which constitutes photosynthetically active radiation. Some organisms have been found to photosynthesize under such spectrum but less efficiently than under solar light, as their photosynthetic apparatus evolved to harvest visible light emitted by the Sun. Around M-dwarfs, such different irradiation might have selected adaptations optimized for harvesting far-red / infra-red light. On Earth, similar selection can be found in Acaryochloris marina strains, constitutively presenting high chlorophyll d content in photosystem II & I, with in vivo absorption peaks beyond 700 nm. Here we tested the Moss Beach strain under a simulated M-dwarf spectrum and a simulated primeval atmosphere - anoxic and enriched in carbon dioxide. Results underline how this permanently red-shifted photosynthetic apparatus does not require acclimation to the stellar spectrum and enables for a strong growth and oxygen production, higher than under simulated solar light. Moreover, cells reflectance spectrum highlights a shift of the canonical red-edge toward longer wavelengths, resulting in a Chl d-near-infrared edge, suggesting a similar metabolism on exoplanets orbiting M-dwarfs could successfully produce both a gaseous biosignature and a characteristic surface biosignature.
]]></description>
<dc:creator><![CDATA[ Liistro, E., Boccia, B., Parenteau, M. N., Kiang, N. Y., La Rocca, N. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719884</dc:identifier>
<dc:title><![CDATA[Is constitutive red-shift an advantage for oxygenic photosynthesis under M-dwarf starlight? Insights from Acaryochloris marina sp. str. Moss Beach]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719861v1?rss=1">
<title>
<![CDATA[
Improved transcriptome assembly of Monarda citriodora reveals candidate HD-ZIP IV transcription factors involved in trichome development and secondary metabolism 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719861v1?rss=1
</link>
<description><![CDATA[
Members of the HD-ZIP transcription factor family play an important role in plant processes, including growth, development, metabolism, and stress response regulation. Among these, the sub-family IV members regulate epidermal cell differentiation, trichome development, and secondary metabolism. Monarda citriodora, an aromatic plant, produces economically important essential oils enriched in thymol. Thymol and other related monoterpenes are primarily biosynthesized and stored in glandular trichomes. Despite its significant economic value, the comprehensive identification of the transcription factor families has not been studied in this plant species. Given the importance of HD-ZIP-IV members in regulating trichome development and secondary metabolism, we identified these members in M. citriodora in the present study. To this end, firstly, we carried out transcriptome sequencing of M. citriodora flowers, and the resulting reads, along with previously sequenced reads, were used to reconstruct a transcriptome assembly. The assembled transcripts represented all major plant parts. Using this improved assembly, HD-ZIP-IV members were identified. Their expression profiles and phylogenetic positions, in conjunction with those of known regulators, identified candidate genes involved in the secondary metabolism and/or trichome development in M. citriodora. Furthermore, through gene co-expression analysis, several McHD-ZIP-IV members were found to be co-expressed with McDXS and McTPS genes. These McHD-ZIP-IV members may serve as key candidate genes for functional analysis to determine the regulation of trichome development in M. citriodora. Taken together, the present study provides a resource for improving M. citriodora using molecular tools.
]]></description>
<dc:creator><![CDATA[ Andotra, S., Shafeeq, K., Pal, K., Majeed, A., Misra, P. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719861</dc:identifier>
<dc:title><![CDATA[Improved transcriptome assembly of Monarda citriodora reveals candidate HD-ZIP IV transcription factors involved in trichome development and secondary metabolism]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719834v1?rss=1">
<title>
<![CDATA[
A MaBBX21-MaGCN5 Histone Acetyltransferase Module Regulates Flavonoid Biosynthesis to Improve Heat and UV B Stress Tolerance in Banana (Musa acuminata) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719834v1?rss=1
</link>
<description><![CDATA[
Flavonoids are important specialized metabolites that contribute to plant pigmentation, stress adaptation, and nutritional value. In banana, a major global staple crop, their accumulation is highly tissue-specific, with very low levels in the edible pulp, and the mechanisms underlying this spatial distribution remain unclear. Here, integrative transcriptomic and metabolomic analyses across vegetative and reproductive tissues reveal that light responsive regulatory networks control tissue-specific flavonoid biosynthesis. We identified a B box transcription factor MaBBX21 as a key positive regulator of flavonoid biosynthesis. Its overexpression enhances flavonoid accumulation, whereas knockdown leads to a reduction in flavonoid levels in banana. Mechanistically, MaBBX21 interacts with MaHY5 and directly activates anthocyanin biosynthesis genes (MaDFR2 and MaANS). It also regulates metabolic flux by binding to the MaWRKY23 promoter, promoting flavonol biosynthesis through activation of MaFLS1 while partially repressing the anthocyanin branch. In addition, MaBBX21 introduces an epigenetic layer by activating the histone acetyltransferase MaGCN5, increasing H3K9 acetylation at target promoters, including MaDFR2, MaANS, and MaBBX21 itself, thereby forming a positive feedback loop. Functionally, MaBBX21 overexpression enhances flavonoid accumulation, ROS scavenging, and tolerance to heat and UV-B stress, whereas knockdown lines show reduced metabolite levels and increased stress sensitivity. Collectively, these results define a MaBBX21 MaWRKY23/MaGCN5 regulatory axis that integrates transcriptional regulation, and chromatin modification to control flavonoid biosynthesis, providing a foundation for improving nutritional quality and stress resilience in banana.
]]></description>
<dc:creator><![CDATA[ Singh, S., Tyagi, S., Naresh, R., Bhambhani, S., Chhatwal, H., Naik, J., Pucker, B., Stracke, R., Pandey, A. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719834</dc:identifier>
<dc:title><![CDATA[A MaBBX21-MaGCN5 Histone Acetyltransferase Module Regulates Flavonoid Biosynthesis to Improve Heat and UV B Stress Tolerance in Banana (Musa acuminata)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.718524v1?rss=1">
<title>
<![CDATA[
The effect of organic amendment composition on zinc and cadmium availability and uptake in wheat crops 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.718524v1?rss=1
</link>
<description><![CDATA[
Organic amendments provide crops with nutrients, but can also add pollutants. Yet the fate of micronutrients such as zinc (Zn) and pollutants such as cadmium (Cd) in soil-crop systems is difficult to predict because of the complexity of amendments added to soils. We performed pot and incubation experiments to determine whether the soil availability, uptake and transfer to grain of Zn and Cd in wheat (Triticum aestivum) are linked to the composition of amendments. Three amendments with highly diverse chemical properties, including varied organic matter (OM) degradability, were applied to a non-contaminated, arable soil. Stable isotopes of 70Zn and 106Cd were used to trace metals taken up from inputs versus soil in wheat biomass. We found the amendment most enriched in rapidly degradable OM (poultry manure) led to the highest wheat uptake of input-derived Zn i.e., 87+/-4 mg Zn (kg soil)-1. This was 2.5 times higher than input-derived Zn uptake from the most degraded amendment (compost). We did not observe an increase in soil available Zn with amendment application. Thus, biotic processes resulting from soil-plant-microbial interactions led to the increase in wheat uptake of input-derived Zn with amendment enrichment in rapidly degradable OM. Amendments led to minimal uptake of input-derived Cd in wheat and did not increase soil available Cd. Furthermore, we found no significant increase in grain Zn and Cd concentrations with amendments compared to the control. Our results highlight how amendment OM composition affects soil availability and wheat uptake of Zn and Cd with organic amendment application.
]]></description>
<dc:creator><![CDATA[ Bachelder, J., Tolu, J., Winkel, L. H. E., Wiggenhauser, M., Frossard, E. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.718524</dc:identifier>
<dc:title><![CDATA[The effect of organic amendment composition on zinc and cadmium availability and uptake in wheat crops]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719781v1?rss=1">
<title>
<![CDATA[
Genetic Characterization of the TAPBP and Its Haplotypic Association with BF2 in the Chicken Major Histocompatibility Complex 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719781v1?rss=1
</link>
<description><![CDATA[
TAPBP is a key chaperone of the peptide-loading complex that facilitates peptide loading onto major histocompatibility complex class I (MHC I) molecules. This study characterized TAPBP alleles in Korean Native Chickens (KNCs), identified novel variants, and evaluated haplotypic associations with BF2. Thirty-six samples representing six KNC lines were genotyped using LEI0258 and the MHC-B SNP panel, and individuals homozygous at both markers were classified into 16 groups. The same samples were subjected to Sanger sequencing of TAPBP exons 3-8. Sequences were assembled and aligned against MHC-B reference haplotypes and the Red Junglefowl reference. Additional comparisons with ''tapasin allele'' datasets enabled the identification of novel variants. Six novel nucleotide variants were detected across exons 3-6, including one nonsynonymous substitution in exon 4 (D251H). This residue corresponds to position Q265 in human TAPBP and lies adjacent to residues involved in MHC I interaction, suggesting potential functional relevance. Furthermore, TAPBP exhibited high haplotype diversity (Hd = 0.93) and moderate nucleotide diversity ({pi} = 0.00892), with exon 5 showing the highest diversity ({pi} = 0.01). B9 was the most frequent haplotype at the nucleotide level, whereas B6/B24 predominated at the amino acid level. Comparison with BF2 data revealed haplotype-dependent pairing patterns: BF2-B9 consistently matched TAPBP-B9, whereas BF2-B6 was associated with distinct TAPBP nucleotide variants, indicating allelic diversification within a shared haplotypic background. Homozygosity at LEI0258 and the SNP panel corresponded with TAPBP homozygosity, supporting marker-based prediction. These findings highlight potential BF2-TAPBP associations and provide a foundation for understanding variation in MHC I peptide loading.
]]></description>
<dc:creator><![CDATA[ Fernando, R., Agulto, T. N., Cho, E., Kim, J., van Hateren, A., Kim, M., Prabuddha, M., Lee, J. H. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719781</dc:identifier>
<dc:title><![CDATA[Genetic Characterization of the TAPBP and Its Haplotypic Association with BF2 in the Chicken Major Histocompatibility Complex]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719829v1?rss=1">
<title>
<![CDATA[
Moderate overexpression of PROTON GRADIENT REGULATION 5 improves photosynthetic performance and plant growth under fluctuating low light in Arabidopsis thaliana 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719829v1?rss=1
</link>
<description><![CDATA[
Cyclic electron transport (CET) around photosystem I (PSI) is essential for maintaining photosynthetic efficiency by balancing ATP/NADPH production and protecting PSI from photoinhibition. Although the PROTON GRADIENT REGULATION 5 (PGR5)-dependent CET pathway is known to be critical under high or fluctuating light conditions, its role under fluctuating low light remains poorly understood. In natural environments, plants frequently experience prolonged low irradiance interspersed with brief sunflecks, making fluctuating low light a physiologically relevant condition. Here, we investigated Arabidopsis thaliana lines with graded PGR5 expression levels to evaluate the dose-dependent contribution of PGR5 to CET activity, photosynthetic regulation, and growth performance under both low light and fluctuating low light conditions. Moderate increase in the PGR5 protein level enhanced CET activity, accelerated photosynthetic induction, improved PSI protection and increased biomass accumulation under fluctuating low light. In contrast, excessive PGR5 accumulation impaired photosynthetic performance and reduced plant growth, indicating that optimal CET capacity requires precise tuning of PGR5 abundance. These results reveal a non-linear relationship between PGR5 protein levels and photosynthetic performance and demonstrate that moderate enhancement of CET improves plant productivity under fluctuating low light. Our findings highlight the importance of optimizing CET capacity to match dynamic light environments and suggest that fine-tuning PGR5 expression could be a promising strategy for improving crop performance under natural canopy conditions.
]]></description>
<dc:creator><![CDATA[ Tanigawa, K., Kodama, H., Okegawa, Y., Shikanai, T., Yamori, W. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719829</dc:identifier>
<dc:title><![CDATA[Moderate overexpression of PROTON GRADIENT REGULATION 5 improves photosynthetic performance and plant growth under fluctuating low light in Arabidopsis thaliana]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.718297v1?rss=1">
<title>
<![CDATA[
The impact of non-cardiomyocyte MYBPC3 expression on the development of hypertrophic cardiomyopathy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.718297v1?rss=1
</link>
<description><![CDATA[
Introduction: Hypertrophic Cardiomyopathy (HCM) is a disease defined by the development of left ventricle hypertrophy. One of the most commonly mutated genes in HCM is cardiac myosin binding protein C (MYBPC3). MYBPC3 protein localizes to the cardiomyocyte sarcomere, but studies have reported detection of both MYBPC3 RNA and protein in non-cardiomyocyte cell populations. Therefore, it was unclear if MYBPC3 expression in non-cardiomyocyte cell populations altered the development of cardiomyopathy caused by MYBPC3 protein deficiency. Methods: We utilized genetically modified murine models with germline deletion of Mybpc3 exons 3 to 5 (Mybpc3-/-) or cardiomyocyte specific deletion of Mybpc3 exons 3 to 5 (Mybpc3fl/fl ; Myh6-Cre). Gene expression was assessed using quantitative RT-PCR. Whole tissue protein levels were assessed using immunoblots. Immunohistochemistry and proximity ligation assays were performed to evaluate in situ protein expression. Echocardiography was utilized to measure left ventricular structure and function. Results: Mybpc3 mRNA was detected in multiple organs including the heart, lung and blood from both humans and mice. Utilizing transgenic murine models with germline or cardiomyocyte specific deletion of Mybpc3 exons 3-5, we discovered that the Mybpc3 mRNA detected in extracardiac locations originated primarily from cardiomyocytes. Likewise, MYBPC3 protein was identified in myocardial tissue but not in other organs and cardiomyocytes were the only cell population in myocardial tissue that had detectable MYBPC3 protein. Importantly, cardiomyocyte deletion of Mybpc3 caused similar pathological myocardial remodeling and alterations in left ventricular function compared to germline deletion of Mybpc3 in all cell populations. Conclusions: Our results show that cardiomyocytes are the primary cell source of Mybpc3 mRNA detected in extracardiac organs and they are the principal cell type responsible for the cardiomyopathy caused by MYBPC3 protein deficiency. These results suggest that selective targeting of cardiomyocytes should be the most efficient approach to treat cardiomyopathies associated with MYBPC3 deficiency.
]]></description>
<dc:creator><![CDATA[ Clavere, N. G., Kim, J. H., Letcher, K. P., Molakaseema, S. T., Silva, K., Pal, S., Becker, J. R. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.718297</dc:identifier>
<dc:title><![CDATA[The impact of non-cardiomyocyte MYBPC3 expression on the development of hypertrophic cardiomyopathy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719576v1?rss=1">
<title>
<![CDATA[
Genome Assembly of the Iconic Samba Mahsuri Delineates Locus-specific Population Structure within Indica Rice 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719576v1?rss=1
</link>
<description><![CDATA[
High-quality reference genomes enable detailed analysis of structural variation and its consequences for genome organization in crops. Here, we present a chromosome-scale genome assembly of Oryza sativa cv. Samba Mahsuri (SM), an elite Indian mega rice variety cultivated for its grain and cooking quality. Using PacBio HiFi sequencing in combination with Illumina reads and Bionano optical mapping, we generated a ~395 Mb assembly (SMv1.0) with 97.7% BUSCO completeness. A robust annotation framework identified 31,138 evidence-guided protein-coding gene models alongside 59,152 ab initio predictions. Comparative genomic analyses revealed extensive macrosynteny with established rice reference genomes, while uncovering pronounced locus-specific sequence and structural polymorphisms. Notably, a complex inversion-match-inversion (IMI) configuration on chromosome 6 differentiates SM from the japonica reference Nipponbare, but not from the indica reference R498. Population-scale analyses of 533 cultivated and 4 wild rice accessions demonstrate that genetic variation within the IMI region produces a markedly sharper and more coherent population structure than is observed in flanking regions or genome-wide, including tight subpopulation-based clustering and segregation of alternative IMI configurations within indica rice. Together, these results establish SMv1.0 as a robust chromosome-scale reference genome sequence for rice and demonstrate how large structural polymorphisms can shape locus-specific patterns of relatedness that diverge from genome-wide ancestry.
]]></description>
<dc:creator><![CDATA[ Rao, D., K, S. K., T, N. S., Khan, E., Sonti, R. V., Tiwari, S., Patel, H. K. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719576</dc:identifier>
<dc:title><![CDATA[Genome Assembly of the Iconic Samba Mahsuri Delineates Locus-specific Population Structure within Indica Rice]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720131v1?rss=1">
<title>
<![CDATA[
The evolution of plant actins 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720131v1?rss=1
</link>
<description><![CDATA[
Why plants have evolved large families of highly similar actin isoforms, and what functional distinctions sustain their retention, remains an unresolved problem in cytoskeletal biology. Actin is among the most ancient and conserved proteins in eukaryotes, yet plant genomes encode an unusually high number of closely related paralogs whose specialization is poorly understood. Here, we reconstruct the evolutionary history of plant actins across the green lineage by combining sequence retrieval, phylogenetics, comparative sequence analysis, and structural mapping. We find that plant actin diversification arose multiple times and, strikingly, relatively late in the history of this ancient protein family. A major duplication produced two deeply conserved seed-plant actin clades, corresponding to the previously described vegetative and reproductive actins; here, we refer to these as Type I and Type II to reflect their phylogenetic relationships. Across the green lineage, increases in actin copy number track key transitions in plant complexity, particularly in tracheophytes. Despite this diversification, only a limited set of conserved substitutions distinguishes major actin lineages. Mapping sequence variation onto actin structures reveals a prominent surface patch that appears permissive to mutation, suggesting relaxed functional constraint, whereas isoform-specific changes cluster at sites likely to influence filament stability, turnover, and treadmilling. A finer-scale analysis in Brassicales pinpoints recent substitutions predicted to alter hydrogen-bonding patterns within monomeric and filamentous actin. Together, our results argue that plant actin diversification is not redundant drift, but a recurrent evolutionary strategy that preserves the actin core while tuning the intrinsic biophysical behavior of f-actin.
]]></description>
<dc:creator><![CDATA[ Lamers, J., Pereira, D., Kaper, M., Sprakel, J. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720131</dc:identifier>
<dc:title><![CDATA[The evolution of plant actins]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719616v1?rss=1">
<title>
<![CDATA[
REVOLUTA regulates cell fate and wall patterning in the fruit endocarp 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719616v1?rss=1
</link>
<description><![CDATA[
Explosive seed dispersal distinguishes Cardamine species from Arabidopsis and depends on polarized secondary cell wall (SCW) deposition in fruit endocarp b (endb) cells. How this SCW pattern is specified and environmentally modulated remains unclear. The polyploid Cardamine chenopodiifolia produces explosive aerial fruit and non-explosive subterranean fruit, creating a tractable system to address this problem. We show light triggers underground fruit to explode by reprogramming endb SCW patterning from uniform to polar. We identify the HD-ZIPIII transcription factor REVOLUTA as a central regulator of endb cell fate, SCW formation, and organ polarity in Arabidopsis and Cardamine hirsuta. In C. hirsuta, duplicated REVOLUTA paralogs are required for endb SCW deposition, while other HD-ZIPIII genes contribute redundantly to cell fate and organ polarity. REVOLUTA over-expression converts polar endb SCWs to uniform, producing non-explosive fruit. Together, these findings reveal a tunable developmental module underlying evolutionary transitions between explosive and non-explosive seed dispersal strategies.
]]></description>
<dc:creator><![CDATA[ Emonet, A., Spatz, I., Kelly, C., Tikhomirov, N., Dunemann, S., Brombach, L., Raissig, M., Pauly, M., Hay, A. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719616</dc:identifier>
<dc:title><![CDATA[REVOLUTA regulates cell fate and wall patterning in the fruit endocarp]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719653v1?rss=1">
<title>
<![CDATA[
Early salt shock uncouples shoot - root acclimation in Lobularia maritima 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719653v1?rss=1
</link>
<description><![CDATA[
Salt stress triggers overlapping osmotic and ionic effects. In halophytes, rapid acclimation can obscure how early responses are coordinated across organs. The use of facultative halophytes and salt shocks provides a useful framework to resolve this transition. We investigated the first 24 h of salt shock responses in the facultative halophyte Lobularia maritima by integrating physiological, ionomic, transcriptional and phytohormonal analyses to resolve organ- and time-dependent acclimation dynamics. Salt shock induced a rapid but transient osmotic effect, with shoot turgor recovery after 8 h. This recovery was associated with sustained osmotic adjustment, proline accumulation and increased Na+ levels in shoots. Conversely, photosynthetic impairment persisted beyond osmotic recovery. Salt exposure rapidly reshaped shoot and root ionomes and was associated with dynamic expression of LmSOS1, LmNHX1, and LmHKT1, consistent with coordinated Na+ partitioning. Oxidative responses diverged between organs; shoots maintained a stable oxidative state, while roots exhibited progressive loss of meristem viability. Abscisic acid (ABA) was strongly accumulated at all time points and emerged as the dominant regulator of early responses. These results show that early salt acclimation in L. maritima is rapid but spatially and functionally uncoupled, combining fast shoot osmotic adjustment with persistent photosynthetic constraints and increased root vulnerability.
]]></description>
<dc:creator><![CDATA[ Gonzalez-Cobo, C., Tolra, R., Charif, G., Bianucci, E., Llugany, M. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719653</dc:identifier>
<dc:title><![CDATA[Early salt shock uncouples shoot - root acclimation in Lobularia maritima]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719605v1?rss=1">
<title>
<![CDATA[
Mechanisms controlling the deposition and dynamics of histone variant H2BE 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719605v1?rss=1
</link>
<description><![CDATA[
Histone variants shape chromatin structure and gene regulation and their deposition and localization in chromatin are tightly controlled. H2BE is the only known widely expressed mammalian H2B variant and localizes to transcription start sites to control chromatin accessibility and cognitive function. However, the mechanisms governing H2B variant incorporation into chromatin remain unclear. Here, we define the regulatory framework controlling H2BE incorporation, localization, and eviction in neuronal chromatin. We identify the BAF remodeling complex and the transcription factor SP1 as key drivers of H2BE deposition at specific genomic loci. We further show that FACT maintains H2BE enrichment at transcription start sites by preventing its distribution into gene bodies, while the histone chaperone NAP1L4 mediates H2BE eviction from chromatin. Comparative analysis with H2A.Z reveals that BAF, SP1 and NAP1L4 exert H2BE specific functions, while FACT functions more broadly across histone variants. Finally, we define the H2BE-dependent transcriptional effects of it chaperones. Together, these findings uncover the first chaperones governing H2B variant incorporation and define a highly complex mechanism responsible for H2BE regulation in chromatin.
]]></description>
<dc:creator><![CDATA[ Sangree, A. K., Feierman, E. R., Perez-Tremble, R., Korb, E. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719605</dc:identifier>
<dc:title><![CDATA[Mechanisms controlling the deposition and dynamics of histone variant H2BE]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.718945v1?rss=1">
<title>
<![CDATA[
An overexpression platform reveals the functional diversity of human KRAB-Zinc Finger Proteins in maintaining cellular homeostasis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.718945v1?rss=1
</link>
<description><![CDATA[
Kruppel associated box zinc finger proteins (KZFPs) form the largest family of transcriptional regulators in mammals, yet most remain uncharacterized. Here we establish a scalable framework to probe KZFP function. An arrayed inducible overexpression screen of 366 human KZFPs in K562 cells identifies factors that alter cellular proliferation, enabling functional prioritization. Integrative transcriptomic, chromatin and proteomic analyses reveal diverse mechanisms, including transposable element linked repression (ZNF43), promoter proximal regulation (ZNF257), and SCAN domain dependent transcriptional activation (ZNF498/ZSCAN25 and ZNF18). These results highlight the functional diversity of KZFPs and provide a strategy for their annotation.
]]></description>
<dc:creator><![CDATA[ Forey, R., Raclot, C., Dorschel, A., Archambeau, J., Planet, E., Bompadre, O., Offner, S., Matsushima, W., van der Goot, F. G., Trono, D. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.718945</dc:identifier>
<dc:title><![CDATA[An overexpression platform reveals the functional diversity of human KRAB-Zinc Finger Proteins in maintaining cellular homeostasis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.19.719523v1?rss=1">
<title>
<![CDATA[
Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.19.719523v1?rss=1
</link>
<description><![CDATA[
Understanding crop population history requires genetic material that predates modern breeding. In rice (Oryza sativa), extant landraces have revealed a broad regional structure within indica, but the historical depth of these patterns remains uncertain. Here, we analyzed a historical collection of rice landraces assembled in Southeast Asia from 1957 to 1958 (henceforth the Hamada collection). Short-read resequencing yielded 66 high-quality historical samples (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the major regional structure previously described for extant landraces was recovered. Within the Hamada collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous mainland Southeast Asian group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to two traditional growth seasons (fifth- and tenth-month rice). The fifth-month rice accessions were assigned to the previously reported distinct Vietnam-I5 cluster, showing that this lineage already existed before modern breeding. Admixture graph, f-statistics, and qpWave analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage with a distinct admixture event that cannot be adequately attributed to sampled indica, japonica, or aus groups. Together, these results show that the present-day regional structure of indica was established before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.
]]></description>
<dc:creator><![CDATA[ Numaguchi, K., Lim, S., Orn, C., Higashikubo, Y., Saito, H., Sato, Y., Ishikawa, R., Gutaker, R. M., Ishii, T. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.19.719523</dc:identifier>
<dc:title><![CDATA[Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.19.719106v1?rss=1">
<title>
<![CDATA[
PSoup: an R package for simulating biological networks from a qualitative perspective 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.19.719106v1?rss=1
</link>
<description><![CDATA[
Mathematical modelling is essential for understanding how complex biological systems respond to genetic, physiological, and environmental changes. Existing approaches, however, often require trade-offs between mechanistic detail, model size, parameter uncertainty, and interpretability. Ordinary differential equation (ODE) models capture biochemical processes with quantitative precision but can demand extensive parameterisation. In contrast, large statistical and machine-learning models rely on substantial datasets and frequently lack mechanistic transparency. Qualitative approaches such as Boolean networks improve scalability but may oversimplify biological behaviour. To address some of these limitations, we present PSoup, an R package that automatically converts knowledge graphs into transparent, parameter-free, qualitative models. PSoup uses algebraic update rules designed around a fixed, biologically interpretable baseline, enabling predictions of relative change across diverse perturbations without requiring kinetic parameters. This design allows PSoup to integrate information across biological scales and from heterogeneous experimental sources. We evaluated PSoup using the well-studied shoot branching network of Bertheloot et al. (2019), which ncorporates hormonal (auxin, strigolactone, cytokinin) and metabolic (sucrose) regulation. Across 78 experimental conditions, PSoup correctly predicted 88.5% of perturbation outcomes, including 89.5% accuracy for unique, biologically consistent comparisons. We further demonstrate how PSoup can distinguish among alternative plausible network topologies, revealing how structural differences influence emergent system behaviour. PSoup offers an intuitive, accessible, and mathematically transparent framework for exploring biological networks. Its capacity to integrate diverse knowledge and test alternative hypotheses positions it as a powerful tool for biological discovery and a valuable complement to existing modelling approaches.
]]></description>
<dc:creator><![CDATA[ Fortuna, N. Z., Lawson, B. A. J., Mitsanis, C., Burrage, K., Beveridge, C. A. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.19.719106</dc:identifier>
<dc:title><![CDATA[PSoup: an R package for simulating biological networks from a qualitative perspective]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719558v1?rss=1">
<title>
<![CDATA[
A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719558v1?rss=1
</link>
<description><![CDATA[
Agrobacterium-mediated transient expression has revolutionized plant research, enabling numerous landmark discoveries across diverse areas of plant biology. Yet this powerful approach remains largely confined to solanaceous species, leaving most economically important crop families without a comparable rapid assay platform. Here, we show that an engineered Rhizobium rhizogenes strain, AS109, mediates efficient transient expression across diverse dicot species spanning multiple taxonomic families, consistently outperforming commonly used laboratory agrobacterial strains. Leveraging the broad host range of AS109, we establish a suite of functional assays in faba bean (Vicia faba), including protein localisation, RNA interference-mediated gene silencing, cell-surface elicitor recognition screens, nucleotide-binding leucine-rich repeat receptor (NLR) activation, and infection cell biology at the host-pathogen interface. We further demonstrate that both singleton NLRs and sensor-helper NLR pairs from Solanaceae retain effector recognition and cell death activity when transferred into faba bean, establishing a rapid platform for evaluating cross-family transferability of disease-resistance genes. AS109 thus provides an accessible and versatile chassis for functional genomics in non-model crops, bridging the widening gap between hypothesis generation and experimental validation across diverse plant species.
]]></description>
<dc:creator><![CDATA[ King, F., Lopez-Agudelo, J. C., Stephens, C., Aung, M. H., Ibrahim, T., Yuen, E. L. H., Chen, A., Eilmann, N. M., Jenkins, S., Vuolo, C., Swee, Y.-N., Liu, W.-J., Bruty, S., Toghani, A., Kuo, C.-H., Lai, E.-M., Kourelis, J., Derevnina, L., Wu, C.-H., Bozkurt, T. O. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719558</dc:identifier>
<dc:title><![CDATA[A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719603v1?rss=1">
<title>
<![CDATA[
Cas9/sgRNA-mediated genome editing of citrus via mature tissue transformation enables both high-efficacy genome editing and early flowering 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719603v1?rss=1
</link>
<description><![CDATA[
CRISPR genome editing has shown tremendous potential in genetic improvement of citrus. So far, citrus genome editing has been conducted using juvenile tissues resulting in genome-edited citrus plants that require multiple years before they can produce flowers and fruit. Here we tested whether citrus genome editing via mature tissue transformation can overcome such a hurdle. CsLOB1 is a susceptibility gene for citrus canker caused by Xanthomonas citri subsp. citri (Xcc). The transcription activator-like effector PthA4 of Xcc activates CsLOB1 by binding to the effector-binding element in its promoter (EBEpthA4-CsLOBP). In Valencia sweet orange, two CsLOB1 promoter alleles are present: TI CsLOBP, and TII CsLOBP. We specifically utilized a CRISPR/Cas9 construct (GFP-p1380N-Cas9/sgRNA:CsLOBP2) targeting EBEpthA4 in TI CsLOBP but not TII CsLOBP to test genome editing efficacy and off-target mutations. GFP-p1380N-Cas9/sgRNA:CsLOBP2 function was first validated using Xcc-facilitated agroinfiltration in Valencia leaves. The construct was subsequently introduced into Valencia mature internodal stem segments via Agrobacterium-mediated transformation, generating three independent transgenic lines (#V2, #V3 and #V5). Targeted mutations in EBEpthA4-TI CsLOBP were detected in all three lines with mutation frequencies of 100%, 21.43% and 41.94% in #V2, #V3 and #V5, respectively, while no mutations were detected in TII CsLOBP. Infection with Xcc{Delta}pthA4:dCsLOB1.3, carrying a designer TALE that specifically activates TI CsLOBP, resulted in reduced canker symptoms in #V2. Importantly, all three EBEpthA4-TI CsLOBP edited lines flowered within 15 months. In sum, these results demonstrate that CRISPR/Cas9-mediated genome modification through mature citrus transformation can achieve high genome editing efficacy and overcome the juvenility.
]]></description>
<dc:creator><![CDATA[ Jia, H., Hu, Z., Wu, H., Duan, Y., Zale, J., Wang, N. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719603</dc:identifier>
<dc:title><![CDATA[Cas9/sgRNA-mediated genome editing of citrus via mature tissue transformation enables both high-efficacy genome editing and early flowering]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719602v1?rss=1">
<title>
<![CDATA[
Isolation and identification of AMF species from selected medicinal plants from BHU Campus 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719602v1?rss=1
</link>
<description><![CDATA[
The objective of this study was to investigate Arbuscular Mycorrhizal Fungi (AMF) associations in selected medicinal plants. In this study 15 commonly used medicinal plants viz., Abutilon indicum (L.) Sweet, Centella asiatica (L.) Urb, Piper longum(L.), Terminalia bellerica (Gaertner) Roxb, Tinospora cordifolia (Wild.) Miers, Withania somnifera, Azadirachta indica A. Juss., Asparagus racemosus Willd., Andrographis paniculata (Burm. Fil.) Nees, Ocimum sanctum L. Eclipta alba, Mentha arvensis, Elettaria cardamomum, Bacopa monnieri and Mimosa pudica were investigated for AMF colonization in the form of arbuscules, vesicles and hyphae from their roots and rhizosphere soil. The rhizosphere soil and root of the commonly used medicinal plants were procured from Banaras Hindu University (BHU). From the study it was clear that AMF spores are abundantly available in the rhizosphere of the plants chosen for this study with spores of Acaulosporaceae and Glomeraceae family being dominant and Funneliformis mossae having the highest relative abundance and isolation frequency among all the AMF species. Keywords:- Medicinal plants, AMF, Relative abundancy, Relative frequency
]]></description>
<dc:creator><![CDATA[ Jha, S. S. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719602</dc:identifier>
<dc:title><![CDATA[Isolation and identification of AMF species from selected medicinal plants from BHU Campus]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719549v1?rss=1">
<title>
<![CDATA[
Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719549v1?rss=1
</link>
<description><![CDATA[
Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal luciferin biosynthesis genes. Unlike the reported autoluminescent plants, which have small, inconspicuous and short-lived flowers, such as tobacco and petunia, Phalaenopsis orchids are ideal for engineering autoluminescent varieties due to their showy, long-lasting flowers. However, it remains unclear whether all Phalaenopsis orchids would become autoluminescent after being engineered with luciferase genes. Here, aiming to screen for suitable cultivars prior to transgenic experiments, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient eFBP2 transformation, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin, caffeic acid and tyrosine, and the infiltration ease of eFBP2-containing inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.
]]></description>
<dc:creator><![CDATA[ Wang, Z., Ma, J., Qiu, J., Lin, L., Wang, X., Chen, L., Du, H., Xie, T., Jia, R., Zhang, Y., Li, B., Ruan, J., Wang, J., Li, Z., Wang, P. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719549</dc:identifier>
<dc:title><![CDATA[Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719581v1?rss=1">
<title>
<![CDATA[
Prolonged cold exposure enhances regeneration potential in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719581v1?rss=1
</link>
<description><![CDATA[
Prolonged cold exposure over winter impacts plant growth and development but its role beyond flowering regulation remains underexplored. In this study, we show that extended cold enhances regenerative capacity, promoting both callus formation and shoot regeneration in Arabidopsis. This enhancement is mediated by the cold-induced AP2/ERF transcription factors C-REPEAT/DRE-BINDING FACTOR 1 (CBF1), CBF2 and CBF3 which interact with the histone acetyltransferase HISTONE ACETYLTRANSFERASE OF THE GNAT FAMILY 1 (HAG1). The CBFs recruit HAG1 to the loci of key regeneration regulators, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5), to promote their expression via histone acetylation. Our findings thus uncover an epigenetic mechanism by which prolonged cold primes plants for enhanced regeneration, highlighting how environmental cues influence developmental plasticity in plants.
]]></description>
<dc:creator><![CDATA[ Hung, F.-Y., Ince, Y. C., Kawamura, A., Takebayashi, A., Chen, Y., Nagae, T., Iwase, A., Takeda-Kamiya, N., Toyooka, K., Shi, D., Moreno-Risueno, M. A., Wu, K., Sugimoto, K. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719581</dc:identifier>
<dc:title><![CDATA[Prolonged cold exposure enhances regeneration potential in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.720031v1?rss=1">
<title>
<![CDATA[
EA-PheWAS: Integrating Phenotype Embeddings with PheWAS for Enhanced Gene-Phenotype Discovery 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.720031v1?rss=1
</link>
<description><![CDATA[
Phenome-wide association studies (PheWAS) enable systematic exploration of relationships between genetic variants and clinical phenotypes derived from electronic health records (EHRs). Conventional regression-based PheWAS treats phenotypes separately and relies on binary phenotype representations, which limits statistical power for rare variants and rare phenotypes and reduces the ability to detect associations with phenotypes that are distributed across clinical codes. To address this limitation, we first developed EmbedPheScan, a phenotype embedding-based prioritization framework that summarizes the phenotypic profiles of rare loss-of-function variant carriers in a continuous embedding space. We then proposed EA-PheWAS by combining these embedding-derived signals with conventional regression-based PheWAS results using the aggregated Cauchy association test. Using the UK Biobank whole-exome sequencing and EHR data, we show that the proposed methods maintain appropriate false-positive control. We then performed genome-wide phenome scans across all genes and across biologically defined gene classes to evaluate EA-PheWAS relative to conventional PheWAS and EmbedPheScan, consistently finding that EA-PheWAS outperformed the other two methods. We illustrate the utility of EA-PheWAS focusing on four genes representing distinct scenarios, including strong-effect disease genes (PKD1, PKD2), genes with large numbers of rare LoF carriers (NF1), and genes with extremely sparse carrier counts (FBN1).
]]></description>
<dc:creator><![CDATA[ Zheng, W., Liu, T., Xu, L., Xie, Y., Jing, Y., Shao, H., Zhao, H. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.720031</dc:identifier>
<dc:title><![CDATA[EA-PheWAS: Integrating Phenotype Embeddings with PheWAS for Enhanced Gene-Phenotype Discovery]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719902v1?rss=1">
<title>
<![CDATA[
Identifying disease-causing mechanisms and fundamental biology of neuromuscular disorder genes through genomic feature analysis 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719902v1?rss=1
</link>
<description><![CDATA[
Introduction: Neuromuscular disorders (NMDs) encompass a broad group of conditions that primarily affect the peripheral nervous system. They are often caused by genetic alterations that impair skeletal muscle function and result in debilitating symptoms. Obtaining an accurate molecular diagnosis remains a challenge, potentially because variants in genes that have yet to be identified as causal. We therefore used advanced computational methods to study the genetic architecture of NMDs and to identify key features that distinguish NMD genes from other genes in the broader genome. Methods: Curated genes implicated in NMDs (n = 639; GeneTable of NMDs) were obtained and merged with a comprehensive set of genomic features for human autosomal protein-coding genes. Machine-learning-based feature selection and ranking were performed using Boruta, along with complementary analytical approaches. These analyses were used to identify the most important genic features (n = 134, subcategories: gene complexity, genetic variation, expression patterns, and other general gene traits) for discriminating NMD genes from other genes in the genome Results: NMD genes exhibit enriched expression in disease-relevant tissues, including skeletal muscle and heart. Additionally, compared with other protein-coding genes, these genes exhibit increased transcriptomic complexity (e.g., longer transcripts and more unique isoforms), contain more short tandem repeats, and show greater variation in conservation across model organisms. Conclusions: This study identified several key genomic features that may distinguish NMD genes from the rest of the genome. This may enhance the identification of novel causal genes and could ultimately facilitate earlier diagnosis and medical management for affected individuals.
]]></description>
<dc:creator><![CDATA[ Martin, A., Llanes-Cuesta, M. A., Hartley, J. N., Frosk, P., Drogemoller, B. I., Wright, G. E. B. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719902</dc:identifier>
<dc:title><![CDATA[Identifying disease-causing mechanisms and fundamental biology of neuromuscular disorder genes through genomic feature analysis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.17.719095v1?rss=1">
<title>
<![CDATA[
Targeting ALA3 with propiconazole regulates plant growth and enables discovery of promising inhibitor leads 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.17.719095v1?rss=1
</link>
<description><![CDATA[
Propiconazole (PCZ) is widely misused growth regulator in leafy Brassica vegetables. Developing green strategies for managing plant architecture has become an urgent agricultural priority. Here, we identified from a membrane-protein-defective yeast library a P4-ATP phospholipid flippase, aminophospholipid ATPase 3 (ALA3), as a target sensitive to PCZ. ALA3 exhibits high binding affinity for PCZ, which inhibits its ATPase activity. Knockdown of ALA3 rendered yeast, Arabidopsis, and Brassica rapa less sensitive to PCZ and conferred a growth-inhibited phenotype. This dwarfing phenotype is mediated through the interaction between ALA3 and CYP51G1 that jointly acts within the brassinosteroid regulatory pathway. Furthermore, we identified lead compounds A01 and A15 as ALA3-targeting agents, and compared to PCZ, they display superior binding affinity and reduced toxicity. Our work establishes ALA3 as a key mediator of PCZ-induced dwarfism and provides dual strategies-creating promising varieties through gene editing and developing targeted green pesticides-to reduce PCZ use.
]]></description>
<dc:creator><![CDATA[ Gao, Q., Wang, S., Guo, D., Song, Y., Yang, Y., Chen, Z., Zhang, X., Chen, R., Xu, H., Lin, F. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.17.719095</dc:identifier>
<dc:title><![CDATA[Targeting ALA3 with propiconazole regulates plant growth and enables discovery of promising inhibitor leads]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.17.719245v1?rss=1">
<title>
<![CDATA[
Linkage and association mapping coupled with pan-genome analyses of Vat homologs reveal QTLs and alleles for aphid resistance in melon 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.17.719245v1?rss=1
</link>
<description><![CDATA[
Aphids threaten crop productivity through phloem feeding and the transmission of plant viruses. Aphis gossypii, in particular, is a widespread and damaging pest of worldwide cultivated melon. Resistance to its emerging CUC1 clone in Europe remains poorly characterized. Here, we dissected the genetic architecture of melon resistance to CUC1 using complementary traits that capture multiple stages of the aphid-melon interaction: plant attractiveness to aphids, acceptance, aphid colonization, and multiplication. Genome-wide association studies (GWAS) in a diversity panel of 174 accessions identified a quantitative trait locus (QTL) for attractiveness on chromosome 6, while analyses in a complementary panel of 212 accessions revealed QTLs for plant acceptance by aphids on chromosomes 3, 8, and 12. Colonization and multiplication traits further highlighted resistance QTLs on chromosomes 5 and 12, the latter supported by both SNP-based GWAS and bulk-segregant analysis. Pan-NLRome k-mer- and graph-based GWAS, together with Vat presence/absence association analyses, provided allele-level resolution of the QTL on chromosome 5, corresponding to the Vat region. Leveraging allelic diversity at this locus, we functionally characterized 20 Vat homologs with four R65aa motifs within their leucine-rich repeat (LRR) domain and demonstrated the capacity of R65aa-type Vat alleles to confer clone-specific resistance. Resistance-conferring alleles limited virus multiplication, such as Cucumber mosaic virus (CMV), when transmitted by five A. gossypii clones, including CUC1. Together, our results revealed multiple genetic determinants underlying quantitative resistance to the A. gossypii CUC1 clone in melon and highlighted the central role of Vat homologs in resistance to both A. gossypii and the viruses it vectors. These findings provide strategic targets for pyramiding resistance loci acting at different stages of the pest life cycle to enhance durable protection against these biotic threats.
]]></description>
<dc:creator><![CDATA[ Belinchon-Moreno, J., Coindre, E., Monnot, S., Berard, A., Canaguier, A., Le-Clainche, I., Mistral, P., Leyre, K., Rittener-Ruff, V., Hinsinger, D. D., Faivre-Rampant, P., Boissot, N. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.17.719245</dc:identifier>
<dc:title><![CDATA[Linkage and association mapping coupled with pan-genome analyses of Vat homologs reveal QTLs and alleles for aphid resistance in melon]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.17.719190v1?rss=1">
<title>
<![CDATA[
Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.17.719190v1?rss=1
</link>
<description><![CDATA[
Plants produce diverse bouquets of specialized metabolites (SMs), yet only a fraction of the vast phytochemical space has been explored to date. Comparative analysis of SM profiles can reveal hotspots of biochemical novelty, while systematic profiling across taxonomic levels does presently not cover large plant families. To study core and accessory SM profiles in the Brassicaceae plant family, we fingerprinted 14 species by Liquid-Chromatography Mass-Spectrometry (LCMS/MS). We develop standardized experimental and computational workflows integrating in silico annotation tools to study consensus compound class and substructure distributions of SMs. Furthermore, we investigate the congruence of chemotaxonomy and species phylogeny across an extended panel of 17 species. Unique metabolite profiles were outstanding in Camelina sativa, Capsella rubella, and B. vulgaris, with the largest unique terpenoid profile annotated in C. sativa, accounting for 33.5% and 55.6% in positive and negative ionization mode, respectively. Substructure motifs were found to overlap with compound class predictions, highlighted for triterpenoids in Camelinodae. Furthermore, dual tissue chemotaxonomic clustering resembled relationships of Brassica subgenomes across tissues. We anticipate that our systematic approach can serve as a blueprint for investigating biochemical diversity in other plant lineages and can boost the characterization of plant natural product pathways.
]]></description>
<dc:creator><![CDATA[ Wolters, F. C., Woldu Semere, T., Schranz, M. E., Medema, M. H., Bouwmeester, K., van der Hooft, J. J. J. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.17.719190</dc:identifier>
<dc:title><![CDATA[Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.718680v1?rss=1">
<title>
<![CDATA[
Maintenance of the leaf cell proliferation boundary by a cell size at division threshold mechanism. 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.718680v1?rss=1
</link>
<description><![CDATA[
The sizes and shapes of organs are established by the combined actions of cell proliferation and cell growth. In plants, the determinate planar leaf is initiated by primordia formation and establishment of abaxial/adaxial polarity (Yamaguchi et al. 2012; Huang et al. 2014; Turchi et al. 2015). Lamina outgrowth is then driven by cell divisions along proximo-distal (PD) and medio-lateral (ML) axes (Rodriguez et al. 2014), established by mutually repressive PD gradients of miRNA and target transcription factors (Debernardi et al. 2014; Schommer et al. 2014; Shankar et al. 2023; Li et al. 2024). These gradients generate proximal regions of competence for cell division and distal regions of growth, endoreduplication and differentiation. The transition from proliferation to growth and differentiation is marked by a cell cycle arrest front (AF), which moves basipetally during leaf growth, progressively restricting proximal proliferative zones as the leaf grows (Alvarez et al. )(Andriankaja 2012. . Intersection of proximal proliferation-promoting gradients with distal growth- and differentiation- promoting gradients may delineate the AF, but its dynamics remain poorly understood at the cellular level. We reasoned that mutants affecting cell proliferation patterns may provide insights into the formation and maintenance of the AF. Spatio-temporal modelling of live imaging data of loss of function mutants of the regulatory peptidase DA1 and its E3 ligase activator BB, which increase cell proliferation (Li et al 1008; Disch ) showed that these proteins establish a threshold cell size at division as functions of distance from the base of the growing leaf and the duration of growth. Loss of their functions increased the persistence of cell divisions and erased the AF. This suggested that the AF emerges from the interaction of threshold areas of cell division with the cessation of division over time.
]]></description>
<dc:creator><![CDATA[ Kelly-Bellow, R., Prior, R. E., Trozzi, N., Majda, M., Carter, R., Hartley, M. S., Grieneisen, V., Maree, A., Smith, R. S., Bevan, M. W. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.718680</dc:identifier>
<dc:title><![CDATA[Maintenance of the leaf cell proliferation boundary by a cell size at division threshold mechanism.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.17.719161v1?rss=1">
<title>
<![CDATA[
Kingdom-wide comparative transcriptomics reveals deeply conserved and predictable stress response programs across Viridiplantae 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.17.719161v1?rss=1
</link>
<description><![CDATA[
How conserved stress responses are across the plant kingdom remains poorly understood. Here, we present a kingdom-wide stress transcriptome atlas of 36 Viridiplantae species, from chlorophytes to angiosperms, across nine abiotic and biotic stresses. The atlas integrates reanalyzed public RNA-seq data with new in-house stress experiments on three species representing basal lineages, yielding 13.6 million differential expression calls from over 3,200 manually curated control-treatment comparisons. We find that ancient gene families respond broadly but moderately, while lineage-specific families respond narrowly but intensely, revealing a division of labor in stress gene deployment. Stress response conservation decays with phylogenetic distance yet remains detectable across more than 700 million years of divergence, with upregulated genes diverging faster than downregulated genes. Functional co-occurrence analysis uncovers a deeply conserved growth-defence tradeoff alongside stress-specific transcriptional rewiring. Conserved stress co-expression modules undergo regulatory subfunctionalization through duplication, with whole-genome duplicate pairs preferentially retained within modules. Finally, DNA and RNA foundation models predict stress responsiveness from sequence alone (auROC 0.755), suggesting a partially conserved cis-regulatory code underlying stress responses across the kingdom.
]]></description>
<dc:creator><![CDATA[ Koh, E., Peh, L. H., Mutwil, M. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.17.719161</dc:identifier>
<dc:title><![CDATA[Kingdom-wide comparative transcriptomics reveals deeply conserved and predictable stress response programs across Viridiplantae]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.17.719158v1?rss=1">
<title>
<![CDATA[
EcoCore; An ecologically diverse panel of Arabidopsis thaliana accessions for studying plant-environment interactions 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.17.719158v1?rss=1
</link>
<description><![CDATA[
Arabidopsis thaliana naturally occurs across a wide geographic range and displays extensive natural variation in several traits including adaptive responses to the abiotic environment (e.g. temperature, drought, salt). Quantitative techniques like Genome Wide Association Studies (GWAS) enable mapping the genetic basis of such environmental responses and benefits from extensive genetic variation, but the size of the chosen diversity panel is often limited by phenotyping capacity. Most studies therefore use subpanels, often based on maximization of genetic diversity. However, this type of selection may overrepresent cosmopolitan alleles and underrepresent rare environment-specific alleles. Here, we demonstrate that the genetic variation in a GWAS subpanel of Arabidopsis thaliana accessions depends almost entirely on the number of accessions in the panel and very little on the composition of the panel. We present the EcoCore panel designed by grouping accessions of the 1001 genomes (1001G; 1135 accessions) collection, based on their native collection environment and selecting an equal number of accessions from each environment. We assessed hypocotyl lengths of plants grown at control and ambient high temperatures (20oC and 28oC) for 913 accessions of the 1001G and mapped these traits with the full 1001G panel versus the EcoCore panel. The EcoCore panel revealed novel genetic associations with hypocotyl length which is attributed to enrichment of alleles from rare environments. We present the EcoCore panel as a manageable resource for studying phenotypic plasticity and the genetic basis of plant-environment interactions.
]]></description>
<dc:creator><![CDATA[ van Eijnatten, A. L., Keijzer, J. J., Trenner, J., Delker, C., Quint, M., Van Zanten, M., Snoek, L. B. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.17.719158</dc:identifier>
<dc:title><![CDATA[EcoCore; An ecologically diverse panel of Arabidopsis thaliana accessions for studying plant-environment interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719541v1?rss=1">
<title>
<![CDATA[
Sex stratified analyses enable new genetic insights into brain imaging phenotypes 
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</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719541v1?rss=1
</link>
<description><![CDATA[
Sex differences are commonly observed in neuroimaging phenotypes and in the risk of brain diseases, yet the underlying genetic mechanisms remain poorly understood. We investigated sex differences in the genetic architecture of 805 neuroimaging phenotypes in 22,950 males and 22,950 females matched for sample size and covariates, and systematically compared sex-stratified with sex-combined genetic analyses. We found eight variant-trait associations with significant sex differences, 235 fine-mapped sex-dominant causal associations, 457 sex-dominant colocalizations with sex hormones, and 96 sex-dominant colocalizations with schizophrenia. Compared with sex-combined analysis, sex-stratified analysis identified 47 new genetic associations, 170 new fine-mapped causal associations, 1,019 new colocalizations with sex hormones, and 191 new colocalizations with schizophrenia. Additionally, sex-stratified analysis improved global heritability and genetic-correlation estimates and enhanced polygenic prediction for certain phenotypes. This work highlights the need to routinely perform sex-stratified genetic association analyses to elucidate sex-specific and sex-shared genetic control of neuroimaging phenotypes and related disorders.
]]></description>
<dc:creator><![CDATA[ Zhang, N., Wang, S., Fu, J., Ji, Y., Liu, N., Qian, Q., Xue, H., Ding, H., Liang, M., Qin, W., Xu, J., Yu, C. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719541</dc:identifier>
<dc:title><![CDATA[Sex stratified analyses enable new genetic insights into brain imaging phenotypes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
