Biology subjects

Harkess, A.

Publications and source records attributed to Harkess, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational challenges compared to autosomes. Here we present a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates: Cytogenetics-By-Sequencing (CBS) tools. Unlike other approaches that typically address one aspect of the sex chromosomes, CBS-tools strives to guide users from the discovery of the heterogametic sex through identifying the sex-determination region (SDR). The core of CBS-tools is automated quantification of sex-specific k-mers in order to predict the heterogametic sex. Using publicly-available datasets, CBS-tools correctly identified the known sex-system of the 31 species tested. Additionally, we used these k-mers to verify and correct phasing of sex chromosomes between haplotypes in species representing different sex-systems. Finally, we used these k-mers to delimit the SDR boundary using an interactive web platform. CBS-tools was developed with previously unexplored sex chromosome systems in mind, but is also suitable for well-examined sex chromosome pairs.

genomics↗

bioRxiv2026

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

Amaranthus L. spans aggressive agricultural weeds, ornamentals, and ancient pseudocereals. Species within the genus vary in morphology, environmental tolerance, and sexual systems, making them well-suited for studying reproductive evolution and plant adaptation. To investigate sex chromosome architecture within the genus, we generated chromosome-level assemblies of a monoecious amaranth (Amaranthus spinosus) and three dioecious species (A. acanthochiton, A. arenicola, and A. floridanus) using PacBio high-fidelity (HiFi) long reads. We paired these data with Dovetail Genomics Omni-C sequencing to achieve haplotype resolution for A. spinosus and A. acanthochiton, and we used reference-guided scaffolding for the remaining two species. The assemblies are highly contiguous, with sizes ranging from 394.24 to 607.10 Mbp, contig N50 from 0.63 to 8.76 Mbp, and scaffold N50 from 22.44 to 37.97 Mbp. Evaluation of the assemblies and annotations revealed 96.3 to 97.6%, and 97.6 to 98.3% BUSCO completeness, respectively. Comparative genomic analysis revealed that the Chromosome 1 inversions and Robertsonian fusion previously reported in A. tuberculatus are conserved in A. acanthochiton and consistent with the architecture of A. arenicola and A. floridanus, suggesting that the evolution of dioecy in this clade predates subsequent speciation. In parallel, multiple homologs of Rf1 on Chromosome 3 of A. spinosus, a monoecious species that exhibits spatial separation of male and female flowers and is closely related to the dioecious A. palmeri, were identified. Together, this study provides foundational resources for advancing evolutionary, ecological, and agronomic research across the genus, including herbicide resistance evolution and weediness traits.

genomics↗

bioRxiv2026

The Polyploid History of Cultivated Dahlia

The cultivated dahlia has a complex evolutionary history that is likely the driver for its diverse floral forms. Previous studies have proposed cultivated dahlia as an allotetraploid, autotetraploid, and in one study an auto-allooctoploid. Here, we used PacBio HiFi long-reads and Dovetail Omni-C reads to assemble and annotate a genome for a tetraploid Dahlia variabilis cultivar Edna C. We identified Edna C as a segmental tetraploid with signature of auto- and allo-polyploidy events based on subgenome-specific repeat partitioning and single-copy gene tree construction within homoeologous groups. Additionally, we identified a cultivated dahlia-specific centromeric monomer shared between Dahlia variabilis Edna C and the Dahlia pinnata Kelvin Floodlight. Based on finding three major chromosome clusters, we propose that Dahlia variabilis Edna C is a segmental tetraploid with evidence of auto- and allopolyploidy.

genomics↗

bioRxiv2026

Newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

Leaf shape varies widely across plant taxa and has repeatedly been shown to affect ecophysiology, interspecific interactions, and fitness. We used population genomics, genome wide association studies (GWAS), and comparative genomics to determine the genetic basis and evolutionary history of an uncharacterized Mendelian leaf shape polymorphism in Ipomoea hederacea. To do so, we assembled a reference genome and generated whole genome sequencing for 123 individuals from 55 populations. We identified a 117 kb indel that perfectly co-segregates with leaf shape by conducting a GWAS and assessing differences in coverage. Syntenic orthologs for genes on the indel were present in five other Ipomoea species with various leaf shapes, indicating the indel is a newly arisen deletion in I. hederacea despite similar leaf shape phenotypes in the other species. More broadly, these results illustrate how a range of leaf shape phenotypes can be produced by distinct genetic mechanisms even in closely related species. Although none of the genes on the indel itself are known leaf shape candidates, there are multiple leaf shape candidate genes in close proximity that are involved in the auxin biosynthesis pathway. Additionally, the genes within the indel have gene functions that could affect other potentially ecologically relevant traits that have previously been shown to be associated with leaf shape in I. hederacea. Therefore, the pleiotropic effects of the indel polymorphism can have important implications for understanding the ecological mechanisms influencing a well-documented leaf shape latitudinal cline in I. hederacea. Significance StatementIpomoea hederacea has been used to investigate the ecological and evolutionary effects of leaf shape because of a well-documented latitudinal leaf shape cline governed by an uncharacterized Mendelian polymorphism in this species. We identified a 117 kb indel that perfectly co-segregates with leaf shape in I. hederacea. The indel appears to be a distinct genetic mechanism than those governing similar leaf shapes in other closely related Ipomoea species. Additionally, possible pleiotropic effects of the indel on other traits has important implications for understanding the ecology and evolution of leaf shape variation in I. hederacea. Therefore, the results and the new genomic resources that we developed will facilitate future work understanding the genetic, developmental, and ecological mechanisms governing leaf shape variation.

plant biology↗

bioRxiv2026

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan

Many hermaphroditic species increase outcrossing rates by partitioning reproduction so that male and female organs mature at different times, a phenomenon known as dichogamy. Previous work has documented that dichogamy in pecan trees is governed by the Mendelian super-gene "G-locus"; however, its non-recombinant sex chromosome-like architecture has impeded quantitative genetic exploration and candidate gene discovery. Here, we probe the genetic drivers of the G-locus through a pangenome-integrated quantitative genomics experiment. We first provide one of the clearest examples to date of mapping bias, where a linear reference-based GWAS discovered 66 off-target peaks while mapping with a pangenome graph reference resolved the known single Mendelian locus. Across six new genome assemblies, the fully haplotype phased G-locus QTL spanned 223-491kb and included 25 candidate gene families. The strongest candidate gene encoded a MATE efflux protein and had dominant allele-specific action during male flower developmental stages. Combined, these candidates and genomic resources provide a powerful foundation for breeding and optimal dichogamy phenotype engineering for future pecan orchards.

genomics↗

bioRxiv2026

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

AO_SCPLOWBSTRACTC_SCPLOWCrimson clover (Trifolium incarnatum L.) is an obligately outcrossing, cool-season annual legume valued for forage and cover cropping, yet genomic resources to support systematic improvement are limited. We performed the first and most comprehensive whole-genome resequencing (WGR) of global crimson clover germplasm to (i) characterize diversity and population structure and (ii) develop a public mid-density enrichment capture panel for breeding applications. A core set of 45 accessions sequenced at [~]50X generated 5.84 million variants, while 149 additional accessions sequenced at [~]2.54X yielded 17.05 million variants. After stringent filtering, we retained 542,790 high-confidence SNPs from the high-coverage dataset and [~]2.4 million from the low-pass cohort. Population analyses (PCA, ADMIXTURE) revealed compact clustering of cultivars, broader dispersion of wild and uncertain-status accessions, and low overall differentiation (FST = 0.0105) with excess heterozygosity (FIS = -0.0592), consistent with obligate outcrossing. Guided by these resources, we designed a 28,913-SNP TWIST hybrid-capture panel enriched for genic regions and evenly distributed across seven chromosomes. This panel is being deployed within Auburn Universitys crimson clover breeding program to support population improvement and cultivar development. The resulting genomic resources provide a reproducible, mid-density genotyping platform for trait discovery, predictive breeding, and diversity monitoring. Together, these advances bring crimson clover genomic resources on par with other legumes such as soybean (Glycine max (L.) Merr.) and alfalfa (Medicago sativa), establishing a robust foundation for genomics-assisted improvement of this key cover and forage crop in U.S. sustainable agriculture. CORE IDEASO_LIWhole-genome re-sequencing of 194 crimson clover accessions revealed >21 M variants. C_LIO_LIHigh-confidence SNP catalogs from 50X and 2X data enable cost-effective genotyping. C_LIO_LIGenetic diversity is weakly structured, with cultivars clustering narrowly by origin. C_LIO_LIA 28,913 SNP enrichment panel delivers uniform genome coverage and >75% genic content. C_LIO_LIThese genomic tools accelerate GWAS, genomic selection, and breeding innovation. C_LI

genomics↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including C. illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes of C. glabra and the published genomes of three other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance. Article summaryCarya glabra (pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest that C. glabra is an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

genomics↗

bioRxiv2025

Elevated CO2 drives epigenetic reprogramming andchromatin dynamics in Arabidopsis thaliana

Atmospheric CO2 levels are rising rapidly, yet how plants respond at the genomic level remains poorly understood. The three-dimensional (3D) organization of chromatin in the nucleus is a key regulator of gene expression and environmental response, and changes in chromatin architecture can be transmitted across generations through epigenetic mechanisms. Here, we report that elevated CO2 is associated with broad 3D chromatin reorganization in Arabidopsis thaliana, spanning scales from chromosome-wide compartment identity to kilobase-resolution Local Chromatin Domains (LCDs) and LCD-Associated Loops (LALs). Using chromatin conformation capture and sequencing (Hi-C) across four mutant backgrounds, we show that these changes exhibit intergenerational persistence in the self-fertilized progeny of plants grown at elevated CO2, and that this persistence is sensitive to the Pol V branch of the RNA-directed DNA Methylation (RdDM) pathway rather than to upstream small RNA biogenesis. At kilobase resolution, we annotated 2,279 LCDs whose borders are enriched for transposable element loci occupied by the chromatin-silencing members Pol V and LHP1, and near a third of LCD borders are LALs. Elevated CO2 is associated with LAL attenuation and altered transcript abundance at LCD borders marked by H3K27me3, implicating coordinated RdDM and Polycomb group (PcG) activity in the chromatin response to elevated CO2. Integrated transcriptome and DNA methylation analysis across all five genetic backgrounds revealed widespread changes in gene and transposable element abundance. These findings support a model in which CO2-associated chromatin reorganization confers transcriptional plasticity through persistent chromatin states shaped by the RdDM and PcG pathways.

plant biology↗

bioRxiv2025

A High-throughput Sequencing Screen to Identify Apomixis in Plants

In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts will lead to the development of new molecular tools for plant breeding. The three most common ways to identify clonal seed production are cytoembryological analyses, genome sequencing to compare the DNA sequence of mother and child, and flow-cytometry seed screens. While flow-cytometry has been the dominant method for more than two decades, it requires specialized equipment, expertise, and occasional troubleshooting. Here we developed a method using short-read skim-seq at moderately low sequencing depths (3X and 6X) to screen diverse Malus genotypes maintained in a USDA germplasm collection for clonal seed production. By sequencing 55 genotypes and 1,216 of their embryos, our screening-by-sequencing method found 17 previously undescribed apomictic genotypes. Five additional apomictic genotypes were detected with flow cytometry data and using internal sequencing controls. This skim-seq embryo screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm, and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.

plant biology↗

bioRxiv2025

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.

genomics↗

bioRxiv2025

Two independent origins of XY sex chromosomes in Asparagus

The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy in the genus, Asparagus is a model taxon for studying genetic sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus [~]3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade that includes garden asparagus (Asparagus officinalis), while the second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade including Asparagus horridus. The XY sex chromosomes and sex-determination genes in garden asparagus have been well characterized, but the genetics underlying dioecy in the Mediterranean Basin clade are unknown. We generated new haplotype-resolved reference genomes for garden asparagus and A. horridus, to elucidate the sex chromosomes of A. horridus and explore how dioecy evolved between these two closely related lineages. Analysis of the A. horridus genome revealed an independently evolved XY system derived from different ancestral autosomes (chromosome 3) with different sex-determining genes than documented for garden asparagus (on chromosome 1). We estimate that proto-XY chromosomes evolved around 1-2 Ma in the Mediterranean Basin clade, following an [~]2.1-megabase inversion between the ancestral pair. Recombination suppression and LTR retrotransposon accumulation drove the establishment and expansion of the Y-linked sex-determination region (Y-SDR) that now reaches [~]9.6-megabases in A. horridus. The new garden asparagus genome revealed a Y-SDR that spans [~]1.9-megabases with ten hemizygous genes. Our results evoke hemizygosity as the most probable mechanism responsible for the origin of proto-XY recombination suppression in the Eurasian clade, and that neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus. Moreover, this work implicates alternative molecular mechanisms for two separate shifts to dioecy in a model taxon important for investigating young sex chromosome evolution. SIGNIFICANCE STATEMENTFlowering plants with separate sexes are ideal systems for investigating genome dynamics underlying the earliest stages of sex chromosome evolution across the tree of life. We use Asparagus as a model to better understand early sex chromosome formation more generally, by investigating how different XY sex chromosomes evolved between two young, closely related clades. Genomic comparisons of garden asparagus and Asparagus horridus (wild related species) revealed distinct evolutionary origins of XY-chromosomes with different sex-determination mechanisms. Whereas the garden asparagus Y-chromosome originally evolved around 3-4 million years ago (Ma), following a small segmental duplication, the Y-chromosome in Asparagus horridus evolved more recently ([~]1-2 Ma) following a large structural inversion between a different chromosome pair. Interestingly, both evolutionary transitions from hermaphroditism to separate sexes occurred as ancestors of garden asparagus and Asparagus horridus independently dispersed northward out of southern Africa.

evolutionary biology↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes (ACTG) program. Originating from a clone of Auburn Universitys historic "Toomers Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

genomics↗

bioRxiv2025

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

O_LIThe North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel pigmentation in the bracts combined with other traits of interest. Because the genetic basis of all traits in flowering dogwood is unknown, combining them using traditional breeding efforts is time, labor, and space-intensive. C_LIO_LIWe developed foundational genomic resources to establish marker-assisted selection within flowering dogwood breeding. We generated diploid, chromosome-scale, annotated genome assemblies for one pink-bracted and red-leafed tree and one white-bracted and green-leafed tree. Additionally, a phenotyping protocol for bract color and presence/absence diagnostic SNPs for bract and leaf color were established. C_LIO_LIWe leveraged these resources to evaluate linkage associations and differential gene expression related to anthocyanin biosynthesis to identify candidate genes regulating bract and leaf pigmentation. Within a 14Mb locus we identified 14 anthocyanin-related candidate genes. Two genes, with MYB (g19533) and RING finger (g19556) binding domains, had both differential gene expression and variants with the expected segregation pattern. C_LIO_LIThese resources will be valuable in combining pink-red bracts with other traits to advance flowering dogwood breeding. C_LI

genomics↗

bioRxiv2025

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

Oxford Nanopore Technologies (ONT) sequencing platforms have enabled scientists to generate sequence reads of 20 kilobase or more, which has facilitated the assembly of complete genomes. Nanopore sequencing involves recording the change in electrical signals as the DNA molecule transverses the pore. Converting this signal information into bases - a process called basecalling - is challenging and require the implementation of machine learning. The models developed for ONT basecallers have continually improved. However, the mean quality of the reads generated fall below a Phred score of 20 (99% accuracy), the target quality for high-quality genome assembly, when used on challenging plant samples. These low-quality base calls limit the ability to conduct de novo genome assembly, accurate phasing of haplotypes, and long-read genotyping. To overcome these shortcomings, we fine-tuned ONTs high accuracy basecalling model using Bonito, an AI-based deep learning basecaller, to develop crop-specific models for five important species in the Rosaceae family. These species include highly valuable tree crops such as apple, peach, pear, plum, and sweet cherry. Through the development of an automated training pipeline, we were able to achieve [~]14% higher mean and median basecall quality, and a [~]20% increase in total reads with Phred scores >15. These results were achieved without significantly affecting the read length N50s and total reads called. As a result, these new crop-specific models will enable members of the Rosaceae genomics community to produce higher quality ONT sequencing data. Furthermore, we are releasing our automated pipeline to facilitate others to train their own organism or crop-specific models.

genomics↗

bioRxiv2025

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for desiccation tolerance. Here, we present a chromosome-level, haplotype-resolved reference genome for M. flabellifolia alongside transcriptomic profiling across a natural dehydration-rehydration cycle. The 1.28 Gb genome exhibits unusually consistent chromatin architecture with putative holocentric chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on chromosome 8. Transcriptomic changes during dehydration varied with the severity of water loss and pointed to early suppression of growth, progressive activation of protective mechanisms, and reversible changes in transcript abundance upon rehydration. Co-expression networks and targeted gene family analyses revealed dynamic regulation of LEA and ELIP genes, with evidence of transcriptome "priming" in hydrated plants, with transcript abundance shifting toward highly disordered proteins during desiccation. Enrichment of ABA and light-responsive cis-regulatory elements in key genes support the existence of conserved stress response pathways. M. flabellifolias rich profile of phenolics and antioxidant genes highlight the overlap between desiccation tolerance and medicinal potential. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia while offering new insights into the mechanisms of desiccation tolerance.

plant biology↗

bioRxiv2025

Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping

Accelerating crop improvement is critical to meeting food security demands in a changing climate. Long-read sequencing offers advantages over short-reads in resolving structural variations (SVs) and aligning to complex genomes, but its high cost has limited adoption in breeding programs. Here we develop a high-throughput, scalable approach for long-read low-pass (LRLP) sequencing and variant analysis with PacBio HiFi reads, and apply it to trait mapping in a complex tetraploid peanut (Arachis hypogaea) genome multi-parent advanced generation intercross. We analyze LRLP using both a single reference genome and a pangraph, using both proprietary and open-source tools to analyze SVs and coverage. An increased number of variants are consistently called for LRLP data compared to short-read data. At 1.63x average depth, LRLP sequencing covered 55% of the genome and 58% of gene space, outperforming 1.68x depth short-read low-pass sequencing, which achieved only 17% and 11%, respectively. Enhanced data retention after filtering for probabilistic misalignment and an [~]8.5x decrease in cost per value further demonstrated LRLPs efficacy. Our results highlight LRLP sequencing as a scalable, cost-effective tool for high-resolution trait mapping, with transformative potential for plant breeding and broader genomic applications.

genetics↗

bioRxiv2024

The evolution of heteromorphic sex chromosomes in plants

Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera >36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species.

evolutionary biology↗

bioRxiv2024

Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Genomic Perspective

The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which 3 lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers (refer to figure 1). This dynamic has been investigated without clear answers for many decades. In this study, we combine known ideas from existing literature with novel methods, tools, and data to generate fresh insights into an old question. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/604804v3_fig1.gif" ALT="Figure 1"> View larger version (8K): org.highwire.dtl.DTLVardef@fcc574org.highwire.dtl.DTLVardef@10759bforg.highwire.dtl.DTLVardef@1950e33org.highwire.dtl.DTLVardef@d7718d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:-C_FLOATNO A simplified phylogeny of green plants/Embryophytes with the respective group and their average chromosome numbers in each group. Heterosporous lineages highlighted in green. C_FIG Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Our results reveal both shared and lineage-specific genomic changes associated with the evolution of heterospory. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. These findings highlight novel insights that may underpin the association between heterospory and reduced chromosome numbers. The general importance of chromosome numbers, structure, and sizes in cellular biology notwithstanding, the association between the emergence of heterosporous reproduction and chromosome number reduction/genome downsizing is not fully understood. It remains unclear why there exists an association between aspects of biology at such disparate levels as reproductive life-cycles and chromosome numbers/genome size. Exploring and answering this conundrum of evolutionary biology can add to our broader understanding of life sciences and of biology at different levels. Applying the novel tools and methods emerging from ongoing progress in biotechnology and computational sciences presents an opportunity to make new inroads into this long-standing question.

bioinformatics↗