Biology subjects

Jenkins, J. W.

Publications and source records attributed to Jenkins, J. W..

At least 19 recordsLinked to original sources

bioRxiv2026

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

Few plants symbolize the European Alps as profoundly as Edelweiss (Leontopodium nivale subsp. alpinum), yet its evolutionary origin and genomic constitution has remained elusive. We present a haplotype-resolved, chromosome-scale assembly of an L. n. alpinum accession from the Central Alps. The 3.15-Gb genome resolved 48 chromosomes in four phased sets with balanced gene and repeat landscapes. Phylogenomics partitioned these sets into two progenitor-derived subgenomes, DE and FG, demonstrating an allotetraploid origin. Comparison with the diploid subspecies L. n. nivale from Southern European Mountains (Appennines) linked DE to this sampled southern lineage, whereas FG derives from another distinct, unresolved diploid progenitor. Chloroplast genomes placed the plastid split between central Alps and Apennine samples in the recent Pleistocene, approximately 20,000 years ago, and LTR insertion-age profiles revealed recent retrotransposon activity consistent with genome shock following allopolyploidization. Although the subgenomes are broadly balanced,large inversions and elevated divergence concentrate on three chromosome groups. On Chromosome 3, structural complexity coincides with FG hypermethylation and DE-biased expression, revealing localized subgenome dominance. Together, these results support previous studies that suggested a westward expansion from the Asian centre of Leontopodium diversity, followed by differentiation and hybridization of closely related European lineages. Our assembly positions Edelweiss as an alpine model for recent allotetraploidy and enables genomic studies of demography, selection and high-alpine adaptation.

evolutionary 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↗

bioRxiv2025

The origins and adaptive consequences of polyploidy in a dominant prairie grass

Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x A. gerardi, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals. Significance statementPolyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi, the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.

plant biology↗

bioRxiv2025

Pan-genome analyses of 226 finger millet-infecting Magnaporthe oryzae strains from eastern Africa reveal two lineages that differ in their genetic make-up, virulence and effector gene content with gene loss driven by homologous recombination between Pot2 elements

Blast disease, caused by the filamentous ascomycete Magnaporthe oryzae, is the main biotic constraint to finger millet production in eastern Africa. M. oryzae is a pathogen on many grass species, but the high host-specificity of blast isolates underscores the need to study pathogen diversity and virulence at the host level. Here, we fill a void on knowledge on finger millet-infecting strains of M. oryzae by sequencing 226 isolates pure-cultured from infected tissues, mainly peduncles and panicles, sampled from field-grown finger millet accessions across Ethiopia, Kenya, Tanzania and Uganda. Phylogenetic analysis showed that eastern African isolates are genetically distinct from Asian isolates, and differentiated into two groups potentially driven by climate variables. One group was dominated by isolates from Kenya and Uganda (KU group), and the other by isolates from Ethiopia and Tanzania (ET group). Analysis of the portfolio of 887 predicted effector genes showed that the KU group had significantly fewer effectors, concomitant with higher virulence levels on the two finger millet accessions tested. We demonstrate that homologous recombination between transposable elements, leading to genomic deletions, plays a key role in gene removal. Transcript profiling of fungal genes in compatible and incompatible interactions revealed upregulation in the incompatible interaction as a characteristic of an estimated 30% of effector genes, including seven of the eight homologs of known avirulence genes from rice-infecting M. oryzae identified in our study. Prioritization of these effectors for functional validation will pave the way for identifying cognate resistance genes and improving finger millet for resistance to blast disease.

plant biology↗

bioRxiv2025

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

O_LIEukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. C_LIO_LIHere, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the speciess current genetic diversity to catalogue variation in genome structure and content. C_LIO_LIAcross this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. C_LIO_LIOur findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. C_LI

genomics↗

bioRxiv2025

Developing future resilience from signatures of adaptation across the sorghum pangenome

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum 1-4, and many other crops that were not homogenized during the green revolution 5, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes 6. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

genomics↗

bioRxiv2025

Multi-season analysis reveals hundreds of drought-responsive genes in sorghum

Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghums remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1,500 transcriptome profiles, across a 3-year field study with replicated plots in Californias Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pan-gene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of drought-responsive genes that responded similarly in all three years of our field study. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.

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

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2024

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch and lignin biosynthetic pathways. To investigate when and how the metabolic innovations known in grasses evolved, we sequenced the genomes of four Poales species, including Joinvillea ascendens and Ecdeiocolea monostachya representing the sister clade to Poaceae. The rho whole genome duplication ({rho}WGD) in the ancestral lineage for all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) responsible for the dual lignin biosynthesis. Integrated functional genomic and biochemical analyses of grass relatives further revealed the molecular basis of key metabolic innovations predating the evolution of grasses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/622220v2_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

O_LIThe legume family originated ca. 70 million years ago and soon diversified into at least six lineages (now extant subfamilies). The signal of whole genome duplications (WGD) is apparent in species sampled from all six subfamilies. The early diversification has posed difficulties for resolving the legume backbone structure and the timing of WGDs. C_LIO_LIIn this study, we report the genome sequences and annotations for Cercis canadensis (Cercidoideae) and Chamaecrista fasciculata (Caesalpinoideae) to help resolve the relative taxonomic placements along the legume backbone, the timings of WGDs relative to subfamily origins, and the ancestral legume karyotype. C_LIO_LIAnalyses of genome assemblies from four subfamilies within Fabaceae show that the last common ancestor of all legumes likely had seven chromosomes, with a genome structure similar to the extant Cercis genome. Our analysis supports an allopolyploid origin of the subfamily Caesalpinoideae, with progenitors involving lineages along the backbone of the legume phylogeny. C_LIO_LIA probable allopolyploid origin of Caesalpinoideae subfamily provides a partial explanation for the difficulty in resolving the structure of the legume backbone. The retained karyotype structure and lack of a WGD in the last 100+ Mya, underscore the utility of the Cercis genome as an ancestral reference for the legume family. C_LI

genomics↗

bioRxiv2024

ZW sex chromosome structure in Amborella trichopoda

Sex chromosomes have evolved hundreds of times, and their recent origins in flowering plants can shed light on the early consequences of suppressed recombination. Amborella trichopoda, the sole species on a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly-contiguous assemblies of the Z and W chromosomes. We identify a [~]3-Megabase sex-determination region (SDR) captured in two strata that includes a [~]300-Kilobase inversion that is enriched with repetitive sequence and contains a homolog of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, like repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is recently derived in Amborella and the sex chromosome pair has not significantly degenerated.

genomics↗

bioRxiv2024

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48,387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the genotype Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large ([~]20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the Williams haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of soybean line Fiskeby III, a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

plant biology↗

bioRxiv2023

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) [~]400 million years ago (MYA). Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no genomic data has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged [~]350 MYA, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications and the resulting intra-genomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape, but also uncover a possibly unique genomic contrast between homosporous and heterosporous species.

genomics↗

bioRxiv2023

Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the heterotrophic stramenopile protist Aurantiochytrium limacinum MYA-1381. Its [~]62 Mbp nuclear genome comprises 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A [~]300 Kbp circular herpesvirus-like genomic element is present at a high copy number. A 269 Kbp related virus-like element was found to reside between two complete sets of rRNA and LORE-TEAR sequences on one end of chromosome 15, indicating recent recombination between the viral and nuclear genome. Our data reveal new types of giant endogenous viral elements originating from herpes-like viruses and existing as either stand-alone or integrated elements.

genomics↗

bioRxiv2022

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

plant biology↗

bioRxiv2022

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of RECQ3 helicase, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results across laboratories and over time. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference.

genomics↗

bioRxiv2021

Multiplex knockout of trichome-regulating MYBs in poplar affects light sensitivity and triterpene accumulation

As the focus for CRISPR edited plants moves from proof-of-concept to real world applications, precise gene manipulation will increasingly require concurrent multiplex editing for polygenic traits. A common approach for editing across multiple sites is to design one gRNA per target; however, this complicates construct assembly and increases the possibility of off-target mutations. In this study, we utilized one gRNA to target MYB186, a known positive trichome regulator, as well as its paralogs MYB138 and MYB38 at a consensus site for mutagenesis in Populus tremula x P. alba INRA 717-1B4. Unexpected duplications of MYB186 and MYB138 resulted in a total of eight alleles for the three targeted genes in the hybrid poplar. Deep sequencing and PCR analyses confirmed editing across all eight targets in nearly all of the resultant glabrous mutants, ranging from small indels to large genomic dropouts, with no off-target activity detected at four potential sites. This highlights the effectiveness of a single gRNA targeting conserved exonic regions for multiplex editing. Additionally, cuticular wax and whole leaf analyses showed a complete absence of triterpenes in the trichomeless mutants, hinting at a previously undescribed role for the non-glandular trichomes of poplar. ONE SENTENCE SUMMARYTargeting conserved sequences with a single gRNA allowed efficient mutagenesis of a multigene family and the recovery of trichomeless and triterpene-free poplar mutants.

plant biology↗