Plant Reproduction

Background and AimsPaspalum notatum reproduces through either sexuality or apomixis, two pathways that may coexist within the same individual and are regulated by interconnected molecular networks responsive to environmental cues. Here, we characterized the transcript structure and expression of BUD SITE SELECTION PROTEIN 13 (BUD13), a component of the RES spliceosomal complex previously reported as differentially expressed in florets of sexual and apomictic plants, as a first step toward testing its involvement in the molecular regulation of the apomixis-sexuality switch. MethodsPreviously generated floral and leaf transcriptomes from sexual and apomictic Paspalum notatum plants, including Oxford Nanopore long-read data, were mined to characterize BUD13 transcript structure and expression. Phylogenetic analyses and in silico mapping were conducted to infer evolutionary relationships and determine the origin of the transcripts. Differential expression was validated by RT-qPCR, while in situ hybridization was used to reveal cell-specific ovule expression patterns. Key resultsBUD13 is expressed in Paspalum notatum florets as a truncated isoform (SHORT) encoding a small protein lacking part of the herpes simplex virus regulatory protein (ICP4) domain. Two SHORT transcripts, SHORT1 and SHORT2, with different 5' untranslated region (UTR) regions, were identified in flowers. SHORT1 was consistently upregulated in apomictic ovules from premeiosis to anthesis. Both transcripts originated from a single genomic locus located in the subtelomeric region of the short arm of chromosome 6. SHORT isoforms with variable structures were detected in other monocots. In situ hybridization showed that, whereas BUD13 was expressed throughout sexual ovules, expression was absent from the female germline of apomictic ovules. A consistent expression was observed in somatic proembryos of aposporous embryo sacs. ConclusionsOur findings reveal structural, spatial and temporal divergence in BUD13 expression between sexual and apomictic reproductive programs, providing new insights into the molecular regulation of asexual seed formation.

Legumes include some of the worlds most significant crop species, such as cowpea (Vigna unguiculata), a subsistence crop widely grown in sub-Saharan Africa. Despite their importance, legume crop improvement is hindered by a lack of high-resolution expression data, particularly for reproductive tissues and cell types. Here, we report on VigExp, a tool for visualising cowpea gene expression datasets. We demonstrate its utility across a range of vegetative and reproductive cell types of varieties IT97K-499-35 and IT86D-1010, which exhibit 93.75% protein sequence conservation and are amenable to stable transformation. This includes previously published transcriptomes of vegetative, floral and seed tissues, combined with developmentally staged male and female reproductive tissues. Also integrated are novel transcriptomes of laser-captured cell types covering reproductive development from meiosis to early embryo formation post-fertilisation. Spatial expression patterns and transcript levels can be visualised through an electronic fluorescent pictograph (eFP) browser. Validated by RT-qPCR, in situ hybridisation, transgenic, and CRISPR gene editing analyses, the predictive accuracy of VigExp matches prior cowpea functional study observations. Critical genes for nodule development and regulation were also identified and their expression patterns established in cowpea. Novel reference genes, constitutively expressed gene promoters for visualization makers/gene-editing, and tissue and cell specific gene promoters for targeting these regions, are identified. The A-type cyclin, VuTAM2, was also identified, with a critical role in male meiosis established. Collectively, VigExp represents an adaptable and updatable resource to support crop improvement in cowpea and other legumes, which are often highly syntenic with respect to genome composition.

BackgroundCell geometry plays a central role in determining division orientation and body axis formation during early embryogenesis in Arabidopsis thaliana. However, quantitative analysis of dynamic three-dimensional (3D) morphology remains challenging because live-imaging studies often rely on two-dimensional (2D) projections, while existing 3D reconstruction approaches, including mesh-based methods, often lose the original orientation information relative to the ovule and require labor-intensive mesh correction. In addition, embryo positional fluctuation caused by floating in liquid medium and continuous growth makes it difficult to analyze temporal morphological changes within a common coordinate system. ResultsWe developed a robust framework for quantitative 3D and four-dimensional (4D; 3D + time) analysis of embryo initial cell (apical cell) morphology. The method first establishes a standardized 3D coordinate system by normalizing cell orientation based on the bottom plane and the optical axis of the observation. Cell morphology is then reconstructed through ellipse-based approximation of serial cross-sections extracted from stacked imaging data, enabling accurate geometric characterization without the need for complex surface mesh reconstruction. To evaluate shape anisotropy, we quantified the apical cell shape in 3D. The framework further supports the characterization of volumetric features of subsequent division, providing a basis for quantifying 3D embryogenesis. ConclusionOur framework provides a simple and noise-reduced approach for quantitative analysis of living cell morphology in 3D. We named the integrated method of combining coordinate normalization with elliptical cross-section-based reconstruction Apical3DTip. This method enables consistent comparison of cell shapes without extensive manual corrections. The method overcomes key limitations of 2D projection-based and mesh-dependent analyses and offers a practical platform for quantifying cell shape and daughter cell shapes in 3D. More broadly, it provides a quantitative foundation for exploring the relationship between cell geometry, morphodynamics, and developmental patterning in living plant embryos.

PremiseSeed size and morphology are critical traits in agriculture, ecology, and genetics, but high-throughput quantification of these traits is often limited by labor-intensive manual measurements or expensive, platform-specific imaging software. Methods and ResultsWe developed SeedMeasure, a lightweight, open-source, and cross-platform command-line tool written in Python that automates the measurement of seed area, length, and width from images. Using a simple imaging setup, the program processes images by correcting for perspective skew, filtering debris, and exports quantitative data alongside quality-check images. We validated SeedMeasure across nine diverse species, ranging from small Arabidopsis thaliana seeds to large Zea mays kernels. The tool quickly handles images using multithreading and demonstrates high reproducibility, yielding low coefficients of variation across repeated runs. ConclusionsCompared to existing software, SeedMeasure is free, offers faster processing through parallel computing, and provides standalone executables that require no programming dependencies. SeedMeasure offers an accessible, cost-effective, and high-throughput approach for rapid phenotypic profiling, making advanced seed morphological analysis available to researchers without specialized laboratory hardware.

In plant breeding and genetics, recent advances in high-throughput phenotyping are beginning to meet the growing demand for large-scale, high-quality phenotypic data that emerged after the development of next-generation sequencing technologies. Recent developments in phenomics have been incorporated into almond breeding programs, facilitating the large-scale acquisition of quantitative phenotypes and the dissection of the genetic architecture underlying morphological and quality-related traits. The implementation of a high-throughput phenotyping platform integrating RGB and hyperspectral imaging with genotyping using the 60K almond SNP array enabled the large-scale characterization of almond populations and the identification of 567 robust marker-trait associations across 66 traits. These analyses revealed two major genomic hotspots on chromosomes 2 and 5 associated with morphological and quality-related traits. These regions harbored biologically relevant candidate genes, including genes associated with OVATE family proteins, brassinosteroid signaling, protein ubiquitination, and acyl-CoA metabolism, as well as other regulators of organ growth, cell proliferation, hormone signaling, and seed development. Furthermore, a novel candidate gene encoding a COMT-like O-methyltransferase involved in lignin biosynthesis was identified and proposed to contribute to shell hardness, a major genetically controlled trait in almond. Together, these findings demonstrate the potential of integrating high-throughput phenomics and genomics to dissect complex traits, identify candidate genes, and accelerate genomics-informed breeding in almond.

In Asteraceae species, the capitulum is a compact inflorescence, featuring a characteristic reproductive structure. Despite the identification of a few key regulatory factors, the transcriptome-level information on the developing capitulum remains limited. Here, we applied single-cell and spatial transcriptome sequencing to investigate the developing Gerbera hybridas capitulum during floret differentiation. We obtained a transcriptomics atlas encompassing different stages of the Gerbera capitulum and analyzed the cellular and spatial dynamics of gene expression. Using marker gene expression and GO enrichment of cluster-specific DEGs, we annotated putative cell types and described changes in gene expression across sampled stages, potentially associated with ongoing developmental processes. We detected activity of previously undescribed MADS-box genes and defined their spatial expression patterns. Notably, the MADS-box gene GAGL12 was found to be enriched in the putative capitulum phloem cells. The GAGL12 protein was shown in yeast two-hybrid assays to interact with several other MADS-domain proteins with hypothesized functions in vasculature development, and further detailed in silico analyses supported a candidate role in the development of capitulum vasculature. Altogether, we provide integrative and dynamic transcriptomic insight into capitulum and floret development and lay a basis for future functional studies of the control and development of this intriguing reproductive structure.

Plant PHAS locus discovery remains challenging because phasiRNA-producing loci must be distinguished from other sRNA-producing regions with high abundance or apparent periodicity. This problem is especially acute for reproductive 24-PHAS loci, which occur within genomes that also produce abundant 24-nt siRNAs from non-PHAS regions. We present Phasis, an open-source Python software tool for plant PHAS-locus discovery from small RNA sequencing data. Phasis combines statistical evidence for phased accumulation with locus-level features and a Register-Resolved Locus Interpretation Layer that evaluates whether candidate loci show coherent phased architecture. Across diverse plant datasets, Phasis recovered validated or annotated 21- and 24-PHAS loci with a strong balance between call-level precision and reference-locus recall, and generally outperformed PhaseTank and ShortStack in matched benchmark analyses. The register-resolved interpretation layer reduced unsupported calls by separating coherent phased loci from ambiguous sRNA-producing regions. In maize dcl5 mutant libraries, Phasis showed strong depletion of 24-PHAS recovery, supporting DCL5-dependent recovery of reproductive 24-PHAS signal. Together, these results support Phasis as a biologically interpretable tool for large-scale discovery of plant DCL-dependent phasiRNA loci.

Flowering time strongly influences crop adaptation, plant architecture, generation turnover, and breeding efficiency, but the functional organization of florigen genes remains poorly resolved in many polyploid orphan crops. Quinoa (Chenopodium quinoa) is a climate-resilient allotetraploid crop with extensive variation in flowering behavior, and genome analyses have identified multiple FLOWERING LOCUS T (FT)-like homologs. However, genome sequence and expression information alone cannot determine which homologs provide effective florigenic output in planta. Here, we combined apple latent spherical virus-mediated overexpression (VOX) and virus-induced gene silencing (VIGS) in quinoa with heterologous expression in Arabidopsis thaliana, domain-swapping analyses, and cross-germplasm validation to functionally dissect quinoa FT activity. Although several CqFT homologs were transcriptionally induced during the floral transition, their functional outputs were markedly unequal. CqFT1A and CqFT1B-1 acted as the major florigenic activators: overexpression of either gene induced rapid and synchronized flowering, whereas CqFT1-VIGS delayed flowering. In contrast, CqFT2A and CqFT2B retained only weak flowering-promoting activity, whereas CqFT1B-2 showed no detectable promotive effect under the conditions tested, revealing a clear functional hierarchy among transcriptionally induced CqFT homologs. Domain-swapping analyses showed that C-terminal variation contributes to, but does not fully explain, functional divergence among CqFT homologs. In late-flowering highland lines, elevated FT input accelerated flowering, induced coordinated floral transition, and shortened the time to viable seed production. These findings identify CqFT1A and CqFT1B-1 as the major florigenic activators in quinoa and establish a functional genomics framework for resolving and modulating flowering-time control in polyploid orphan crops.

Ovate Family Proteins (OFPs) are a class of plant-specific, negative nuclear transcriptional regulators characterized by conserved C-terminal OVATE domain. This study on comparative functional characterization of two head-to-head arranged OFPs - AtOFP2 (Ovate-OFP with full ovate domain) and AtOFP17 (Ovate-Like OFP with partial ovate domain) provides critical insight into how structural variations in ovate domain leads to functional divergence. Detailed phenotypic analysis of 28 physical and physiological traits of loss- and gain-of-function mutants revealed that both genes act as broad, pleotropic repressors of plant growth and development. Removal of repression in knock-down mutants of both genes exhibited reduced duration of seed dormancy, faster rate of germination and growth, bigger plants and significantly higher seed yield. In contrast, constitutive over-expression showed a generalized repressive nature of both genes, with nuanced differences for fine tuning of specific traits. For example, both genes showed antagonistic behaviours on root hair architecture. AtOFP2 act as a strong repressor of root hair development whereas AtOFP17 is a stronger repressor of hypocotyl and root cell architecture. AtOFP17 owing to partial ovate domain exerts a mild level of repression throughout life span as indicated by smaller plants and lesser yield in knock-down AtOFP17 mutants. On the contrary, AtOFP2 exerted a much stronger repressor effect in which > 90% over-expression mutants died at the juvenile stage ; the survival of remaining 10% is probably owing to activation of dosage-dependent feedback loop mechanism as indicated by normal growth of mature plants, and is also evident by transcriptome data. Transcriptome analysis of roots of 7-day old seedling of knock-down and over-expression mutants of AtOFP2 showed downregulation of OFP2 in over-expressed mutants. However, severely stunted phenotype indicated presence of stable OFP2 protein to exert effects. Analysis of DEGs in OFP2 mutants revealed that it acts as an important regulator working at intersection of hormonal signalling affecting critical genes required for auxin, cytokinin, GA, BR and ABA functioning. Perturbations across hormonal signalling pathways affects cell wall remodelling factors such as EXPANSINS, Xyloglucan hydrolases (XTHs) and cellulose synthases (CSLs) causing overall stunted growth; and epidermal patterning genes such as WER, GL1, EGL3, TTG1 leading to severely reduced root length and root hairs. Significantly, functional analysis of this master regulator highlighted a significant economic potential. Knockdown of both these genes relieves their natural repression on reproductive traits, leading to longer siliques, bigger and heavier seeds, and substantially increased overall seed yield, positioning AtOFP2 and AtOFP17 as highly valuable targets for agricultural crop improvement.

Celiac disease (CeD) is an immune-mediated condition triggered by wheat gluten in genetically predisposed individuals. The immune reaction in people with CeD is driven by particular gluten amino acid sequences, or immunogenic epitopes. Some of these epitopes elicit strong immune responses in the majority of CeD patients and are designated as immunodominant epitopes. Previous research has shown correlations between the amount of immunogenic wheat epitopes consumed and the onset of CeD, suggesting that reducing wheat immunogenic epitopes may reduce CeD incidence at the population level. Gluten consists of gliadins and glutenins, with gliadins having the majority of the immunodominant epitopes and glutenins playing a major role in dough strength and breadmaking quality (BMQ). This study used radiation-induced deletions, chemical mutagenesis, and natural variation in wheat (Triticum aestivum) to generate genetic stocks with reduced immunogenic epitope content. Most lines were developed in the wheat cultivar Summit, for which we produced a full genome assembly and annotation. We used exome capture to characterize these deletions and identify prolamins located within and outside the deletions. We combined different deletions and developed molecular markers to facilitate their deployment. For chromosome arms 1BS and 1DS, we generated two alternative lines: one lacking immunogenic epitopes for the development of CeD-safe genetic stocks for research purposes, and another retaining selected glutenins for breeding commercial lines with reduced immunogenicity and adequate BMQ. By making these non-transgenic genetic stocks publicly available, we aim to accelerate the development of wheat varieties with reduced immunogenicity and, eventually, a fully CeD-safe wheat.

Auxin is a key phytohormone that regulates all aspects of plant growth, development, and environmental responses, making the precise analysis of its distribution and signaling essential for understanding plant adaptation and physiological processes. However, despite the agricultural importance of oilseed rape (Brassica napus), the lack of robust, species-specific molecular tools limits detailed studies of hormone signaling in this crop. Here, we developed and characterized reporter systems for the sensitive visualization and quantification of auxin distribution and signaling in B. napus. The DR5cc auxin signaling reporter and a novel synthetic auxin-responsive reporter, BIP3, assembled from promoter fragments of three oilseed rape IAA genes, were generated to drive GUS expression. In hairy roots, both reporters showed auxin-responsive expression in the root apical meristem that became broader after auxin treatment. In transgenic seedlings, flowers at anthesis, and 12-day-old embryos, DR5cc exhibited a more defined expression pattern than BIP3. To monitor real-time auxin dynamics under abiotic stress, DR5cc fluorescent reporters were employed in hairy roots. Mannitol and NaCl treatments induced a time-dependent increase in fluorescence, peaking at 6-12 h before returning to basal levels after 24 h. Furthermore, dual-reporter assays enabled simultaneous monitoring of auxin and cytokinin signaling, revealing distinct hormone-specific spatial responses in hairy roots. Finally, we established a quantitative DII (qDII) reporter system using degron domains from B. napus Aux/IAA proteins, providing a high-resolution quantitative readout of auxin depletion. Together, these reporter systems enable spatial, temporal, and quantitative analyses of auxin dynamics during development and stress adaptation in oilseed rape.

Elongating rice internodes present a developmental gradient from dividing meristem to mature cells, providing an elegant pseudo-time course for study of plant vegetative development. We tested the hypothesis that DNA methylation regulates gene expression during rice internode development by integrating RNA-seq and bisulfite DNA sequencing across eight internode segments. Previously described topologically associated chromatin domain borders aligned with transcription start sites of constitutive expressed genes. CpG and CHG differential methylation was enriched in young segments, consistent with maintenance methylation; whereas CHH methylation showed similar differential abundance in young and old segments. CHH and CHG methylation in upstream regions, CpG methylation within gene bodies, and any methylation in 5' and 3' untranslated regions were permissive of moderate to high gene expression. Very low expression was associated with CpG methylation upstream, CHG and CHH methylation within gene bodies, and CpG and CHG methylation downstream. A nonrandom subset of genes, including cell wall-related glycoside hydrolases, lignin and tricin biosynthesis enzymes, and WD40 proteins, showed methylation-expression correlations, with expression changes enriched in triple-marked elements. These results suggest that internode phenotypes of DNA methylation machinery mutants relate to alteration of specific target genes, opening approaches for grass culm improvement for lodging resistance and biomass production.

Crop photoperiodism models assume that flowering time is primarily controlled by daylength, yet many field observations contradict this view. We previously proposed an alternative framework integrating daily changes in sunrise and sunset times (dSR and dSS). Variety trials in Madagascar and in Argentina supported this concept: mid-late sorghum varieties from the northern hemisphere flowered late or very late when sown in November and December, consistent with the higher dSR/dSS values of the southern hemisphere summer. One Malian variety, sown monthly over six years in West Africa, exhibited high interannual variability in flowering time when sown between November and February. This revealed that up to four photoperiodic responses -- two quantitative and two qualitative, occurring at different times of the year -- may coexist within a single late photoperiod sensitive variety. All responses use only dSR and dSS cues. The qualitative responses are triggered by an internal phasic coincidence, which is set by a linear relationship between dSR and dSS at the onset of plant photoperiod sensitivity, and between dSR+dSS at panicle initiation. The research model fitted data from 28 varieties grown in Mali well. It also accurately fitted the duration to PI observed in three varieties sown at tropical and temperate latitudes. HighlightThe seasonal photoperiodic adaptation of flowering time in sorghum plants may rely on several signal transduction pathways regulated by sunrise and sunset times rather than day length.

The availability of pangenome and resequencing of wheat collections have facilitated the discovery of gene-trait associations in wheat. Yellow stripe-like (YSL) proteins play a key role in the uptake and translocation of metals and yet have not been fully identified and analyzed at the genome-wide level in wheat. In this study, 26 TaYSL genes were identified and divided into four distinct clades, each clade sharing similar domains and motif compositions. Most genes were upregulated under iron deficiency, whereas homoeologs of TaYSL1 were downregulated. Both SNP-based and haplotype-based association studies were used to dissect the role of TaYSLs underpinning grain iron contents (GFeC) and zinc contents (GZnC) in wheat. TaYSL6-2B and TaYSL16-1A haplotypes showed strong association with GFeC, and TaYSL14-6A showed strong association with GZnC in multiple field trials. The distribution of favorable haplotypes in global wheat collection of [~]3000 accessions showed that majority of haplotypes were more prevalent in landraces and winter wheat compared to modern cultivars and spring types, indicating their potential for use in breeding. The combination of favorable haplotypes of three YSL genes associated with GFeC and GZnC were very rare, and most of the wheat accessions has single or double favorable haplotypes. These findings provide the first comprehensive characterization of the TaYSL gene family in wheat and identify significant SNPs and elite haplotypes that can be utilized for genetic improvement and biofortification.

Intraspecific hybridization in allopolyploid plant genomes has the potential to induce non-additive changes in gene expression and DNA cytosine methylation, partly through interactions among divergent parental subgenomes. However, the extent to which intraspecific hybridization reshapes gene expression, coordinates homoeolog regulation, and remodels methylation in higher-order polyploids remains poorly quantified. To address this, we sequenced seedling leaf transcriptomes and methylomes from two parental cultivars of hexaploid bread wheat (Triticum aestivum L.) and their hybrids. More than 40% of genes were differentially expressed between hybrids and parents, although many were not differentially expressed between the parents themselves, consistent with complex trans-regulatory effects in the hybrid genome. This effect was more pronounced for homoeologs whose relative expression differed between the parents. These expression shifts often occurred simultaneously across all three homoeologs within triads, reducing homoeolog expression bias (HEB) in the hybrids. CG methylation levels were similar between the parents and hybrids in regions of low genetic divergence and in transposable element (TE)-rich regions, whereas CG sites in gene-rich regions showed more additive inheritance (hybrids intermediate between parents), particularly when parental haplotypes were themselves divergent. TE and gene body methylation (gbM) was strongly conserved in parents and hybrids. gbM was associated with more balanced homoeolog expression and fewer non-additive expression changes. CHH methylation showed overdominance, whereas non-conserved CHG methylation was enriched in TE-rich regions, suggesting that non-CG remodeling may reflect parental differences in TE and small-RNA content. Our results show that intraspecific hybridization within a hexaploid species can generate non-additive changes in gene expression and DNA methylation in seedling leaf tissue, while the presence of homoeologous genes, parental HEB, parental genetic and methylation divergence, and genomic location have varying levels of influence on expression or methylation remodeling.

Accurate segmentation of plant disease symptoms is essential for crop monitoring and phenotyping, yet it typically requires costly pixel-level annotations. Weakly supervised semantic segmentation (WSSS) alleviates this burden using image-level labels, but its performance depends on the quality of spatial priors such as class activation maps (CAMs). We investigate whether text-guided segmentation with the Segment Anything Model 3 (SAM3) can serve as an alternative weak supervision signal. Three pseudo-mask generation strategies are compared: (i) CAMs refined with SAM or SAM3, (ii) zero-shot text-guided SAM3, and (iii) a hybrid approach combining weak spatial cues with text prompts. The resulting pseudo-masks are used to train a DeepLabV3 model. Text guidance alone matches or outperforms conventional WSSS, achieving up to 0.46 IoU without spatial supervision and 0.61 IoU on a public dataset, although performance is sensitive to text prompt formulation. The hybrid strategy improves robustness, reaching 0.50 IoU on the primary dataset and 0.58 IoU on the additional dataset while reducing prompt sensitivity. Overall, text guidance is a promising alternative to conventional weak supervision, while hybrid approaches provide a more robust solution for plant disease segmentation.

Lima bean (Phaseolus lunatus) is a broadly adapted, economically important leguminous crop and a susceptible host of root-knot nematodes (Meloidogyne spp.; RKN), which are a devastating plant pathogen in agricultural systems worldwide. To date, there have been few studies to elucidate the genetic determinants of RKN resistance in lima beans. Understanding the genetic mechanisms underlying resistance is essential for improving resistance traits and incorporating them into lima bean breeding programs. To assist in marker-assisted selection, we aimed to identify and map quantitative trait loci (QTLs) conferring RKN resistance-related traits. Three recombinant inbred line (RIL) populations were used in this study. Three populations were derived by crossing two RKN-resistant parents with the same RKN-susceptible parent and with each other. All populations were genotyped using genome-wide single-nucleotide polymorphism (SNP) markers. Each population was screened for root galling (RG) and RKN egg reproduction (ER) in response to M. incognita and M. javanica in greenhouse experiments. Three major QTLs were detected and mapped on chromosome Pl04 (QRk-pl04.1), Pl05 (QRk-pl05.1) and Pl10 (QRk-pl10.1) across populations. Among them, QRk-pl05.1 and QRk-pl10.1 affected levels of RG and ER of both RKN species, while QRk-pl04.1 suppressed root galling and reproduction responses of M. incognita but not of M. javanica. These chromosomal regions defined by flanking markers will help guide marker-assisted breeding and gene discovery for broad-based RKN resistance in lima beans.

Poplar (Populus spp.) is a model system for tree biology. Specifically, P. tremula x P. alba INRA 717-1B4 (hereafter "poplar 717") has become an important platform for functional genomics and synthetic biology due to its rapid growth and ease of transgenesis. Here, we present a single-cell RNA-seq atlas of the poplar 717 shoot, including apical meristem, primary and secondary stems, and three stages of leaf development. Analysis of ca. 159,000 cells resolved 40 transcriptionally distinct clusters representing 7 major cell types, providing a high-resolution view of shoot development and tissue organization. We focused on the epidermis which constituted >15% of cells in the shoot atlas for in-depth characterization of epidermal heterogeneity. By integrating known marker genes with transcriptomic signatures consistent with established poplar leaf phytochemistry, we annotated epidermal cell subclusters corresponding to developmental stages, spatial location, and specialized cell types, including a distinct population of non-glandular trichomes. Coupling the single-cell RNA-seq atlas with bulk transcriptome data from glabrous mutants enabled the identification of novel trichome markers. Experimental validation of a representative trichome-specific promoter established a tool with potential to support cell type-targeted-metabolic engineering. We provide the poplar 717 atlas to the community through the BioPoplar Atlas Viewer (http://bio-poplar-atlas.com), providing a platform to explore the poplar transcriptome at single-cell resolution and a foundation for data-driven cell type-aware genetic engineering strategies in poplar.

Survival analysis is a workhorse assay in Drosophila research to evaluate somatic fitness. It is indispensable in the study of ageing and insightful in immunity, metabolism, radiobiology, toxicology, ecology, and others. While conceptually simple, lifespan measurement is labour-intensive because it requires the continuous manual maintenance of large experimental cohorts. Here, we describe Drosben, an approach that combines a 3D-printed device to transfer flies from several vials simultaneously, a paper system for quick data recording and accompanying software that automatically digitalises life tables for analysis. We show that using Drosben reduces the time investment to perform lifespan assays by ~85%, with improved speed regardless of experience handling Drosophila vials. Using Drosben, we address the effects on longevity of chronic feeding of indole-acetic acid (IAA), naphthalene-acetic acid (NAA) and trimethoprim (TMP) -- compounds used to control heterologous targeted protein degradation systems. We find that IAA and NAA have noticeable deleterious effects while TMP has a small protective effect specifically in females. We further show that strong static magnetic fields do not affect Drosophila lifespan. Our work suggests that Drosben can cheaply accelerate research where lifespan is used as a life history trait.

The shift from outcrossing to self-fertilization is a common evolutionary transition in flowering plants. The genus Capsella, comprising the obligate outcrosser C. grandiflora and two self-fertile species, C. rubella and C. orientalis, provides a powerful system to explore genomic consequences of mating system shifts. Despite its utility, existing genomic resources in Capsella are fragmented, incomplete, and particularly deficient in repetitive genomic regions, hindering the study of transposable element (TE) dynamics and gene annotation. Here, we present high-quality, chromosome-scale, near-gapless genome assemblies for C. grandiflora, C. rubella, and C. orientalis. Leveraging these improved genomes, we created high-quality genomic resources for the Capsella genus by performing comprehensive, de novo annotations of protein-coding genes and TEs. Comparative genomic analysis among these species reveals differences in TE abundance, position, and production of small RNAs. These resources provide an unprecedented opportunity to explore how mating system transitions influence genome architecture, TE behavior, and gene evolution. This research also developed a static online platform for Capsella genomic resources, Capsella Database (CapBase, www.capsella.uk), to support community use of these resources. Our findings advance understanding of the genomic impacts of selfing and establish a robust foundation for future research into genomics, epigenomics, and evolutionary biology within Capsella and related plant systems.