Biology subjects

Grimwood, J.

Publications and source records attributed to Grimwood, J..

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

Chromosome-level Atlantic switchgrass assemblies reveal a supernumerary B-Chromosome with transcriptional and evolutionary impacts

Supernumerary B-Chromosomes are extra genetic elements that frequently deviate from Mendelian inheritance to ensure their own survival. Their evolutionary origins and biological impacts within natural plant populations remain largely unexplored. Switchgrass (Panicum virgatum) is a model for studies of local adaptation, but reliance on a single reference genome has limited the detection of lineage-specific genomic content. We generated chromosome-level genome assemblies from the diverged Atlantic switchgrass subpopulation and discovered a previously undetected genomic element: a ~34 Mb supernumerary B-Chromosome, validated by Hi-C contact mapping and long-read depth, which indicates two to four B copies per nucleus. The B-Chromosome has a bipartite architecture including a gene-rich, single-copy proximal region (~8 Mb) and a repeat-rich, gene-poor distal region (~27 Mb) dominated by LTR/Ty3 (Gypsy) elements and punctuated by Mutator TIR peaks. High-resolution mapping reveals a highly rearranged chimera of fragments from multiple autosomes, biased toward the N-subgenome. Intact LTR retrotransposons on the B-Chromosome are younger than those on the A-Chromosomes, especially in its distal region, consistent with a B-Chromosome that arose and expanded within the Atlantic lineage. Population screening and phylogenetic analysis indicate that the B-Chromosome is largely restricted to the Atlantic subpopulation and likely has a single origin. In a typical family, 70% of open-pollinated progeny of B-positive maternal plants were B-positive, with substantial variation among families. Finally, B-Chromosome presence is associated with expression differences in A-Chromosome genes that differ between genetic backgrounds. Together, our results show how accessory chromosomes contribute to the evolutionary and genomic diversity of natural plant populations.

genomics↗

bioRxiv2026

Pangenomics and machine learning reveal genetic variation to optimize carotenoids in sorghum grain

Enhancing grain carotenoid concentration to increase yellowness and provitamin A content in sorghum (Sorghum bicolor [L.] Moench) is a major breeding objective across sub-Saharan Africa. Carotenoid breeding is constrained by costly post-harvest phenotyping and can be accelerated through genetic markers that capture functional variation in key carotenoid biosynthesis genes. Zeaxanthin epoxidase (ZEP) is a major gene controlling sorghum grain carotenoid accumulation, and SNP-based KASP markers facilitate selection of high-carotenoid grain, although quantitative variation remains among lines carrying the favorable allele. We hypothesized that additional functional variation within ZEP and other carotenoid biosynthesis pathway genes contributes to this variation and can be revealed by a pangenome-informed analysis. Using a 33-member pangenome reference, we characterized sequence and structural variation at ZEP and other key carotenoid biosynthesis genes and applied pangenome-derived genotyping to study marker diversity associated with carotenoid accumulation. Evaluation of ZEP in the pangenome reference revealed previously uncharacterized structural variation that is absent from the BTx623 primary reference genome. A pangenome-based association analysis identified genetic markers associated with the accumulation of carotenoids which were specific to particular pangenome reference members, including in RTx430 and SRN39, both yellow endosperm lines. Machine learning identified markers in ZEP, {beta}-OH, ZDS, and Z-ISO as the most predictive for all carotenoid traits, suggesting a multi-locus genetic architecture underlies the accumulation of carotenoids in sorghum grain. By integrating sorghum pangenomic resources with machine learning, this study establishes a framework for pangenome-accelerated trait discovery and identifies new genetic targets for carotenoid biofortification in sorghum.

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

Paralog diversification masks conserved diel regulatory programs during cold acclimation in Brassica rapa

Plant stress responses occur within daily cycles of physiology, metabolism, and growth, making timing a critical dimension of acclimation. In Arabidopsis, circadian and diel regulation influence responses to abiotic stress, including cold, but how this temporal regulation is conserved, diversified, or expanded in crop genomes remains unclear. This question is especially challenging in Brassica rapa, which underwent a genome triplication after diverging from Arabidopsis, resulting in multiple retained paralogs that can be grouped by Arabidopsis orthology and ancient homeologous relationships. Here, we generated a B. rapa pangenome spanning six morphotypes and used it to profile diel (24 h) cold acclimation responses across diverse accessions differing in freeze tolerances. Cold altered peak expression time for thousands of genes, which we grouped into distinct phase-change groups. Circadian leaf movement assays revealed accession-specific differences in clock period and temperature compensation under cold, suggesting that altered clock behavior may contribute in part to the diel transcriptome retiming. At the individual gene level, inferred gene regulatory networks (GRNs) were highly accession-specific and lost shared connectivity under cold stress. However, grouping these paralogs by their Arabidopsis orthologs revealed a highly conserved regulatory architecture that was otherwise masked by paralog diversification. Integrating these networks with functional pathways identified key candidate regulators of retimed processes, including modules linked to nighttime phosphorylation and daytime photosynthesis. Finally, analyzing conserved noncoding sequences across the pangenome prioritized specific regulatory targets within cold-retimed groups. Together, these results demonstrate that cold acclimation in B. rapa is shaped by a combination of diel retiming, paralog-specific regulation, and deeply conserved programs.

plant biology↗

bioRxiv2026

Spliceosome loss in the red tide ciliate Mesodinium rubrum presents a symbiotic cul-de-sac

Mesodinium rubrum, a marine microbial eukaryote associated with some of the largest red tides on Earth, has the remarkable ability to commandeer the plastids, mitochondria and nuclei from the alga Teleaulax amphioxeia for photosynthesis. Here we report analyses of assemblies of M. rubrums two nuclear genomes. Unexpectedly, M. rubrum appears to have completely lost its spliceosomal introns, most spliceosomal molecules, and the key genes for an intron splicing-associated process, Nonsense-mediated mRNA Decay (NMD). In contrast, non-spliceosomal tRNA introns have been retained, as have thousands of intron analogs spliced out of DNA during ciliate somatic genome development (internal eliminated sequences - IESs). Intron-containing genes, especially from intron-rich species like T. amphioxeia, would likely be defunct if horizontally transferred to a host without a spliceosome like M. rubrum, and thus we propose that introns can be a roadblock to progressive endosymbiotic genomic integration.

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↗

bioRxiv2025

Rapid and repeated evolution of myosin copy number in threespine stickleback

Copy number variants at genomic loci evolve at a high rate, are linked to many different diseases, and play a role in adaptive evolution in humans and other organisms. Here we show that stickleback fish from freshwater environments have rapidly and repeatedly evolved an expanded number of copies of a gene family involved in muscle development, Myosin Heavy Chain 3 Cluster C (MYH3C), compared to marine populations. Differences in copy number between marine and freshwater fish are maintained even in the presence of gene flow, suggesting that MYH3C changes represent adaptive divergence between ecotypes. Copy number expansion occurs by tandem duplication of MYH3C coding and regulatory regions on the stickleback sex chromosome. We identify a muscle regulatory enhancer within the expanded MYH3C region and show that elevated copy number is associated with developmental and tissue-specific increases in corresponding mRNA expression levels in skeletal muscle. Common MYH3C clusters include 3-, 4-, 5-, and 6-copy variants that likely evolved through a combination of microhomology-mediated break repair and non-allelic homologous recombination. Our results provide a new example of copy number changes in a wild species and identify CNVs as potential "hotspots" of repeated adaptive evolution.

evolutionary biology↗

bioRxiv2025

Leveraging species-wide variation and patterns of adaptation to inform pecan crop improvement efforts

The genetic basis of adaptation is a fundamental question in evolutionary biology, and understanding how species will be able to adapt to changing conditions across their range has important implications for conservation and agriculture. To accurately interrogate the genetics of adaptation and assess the adaptive capacity of a species requires also characterizing the ways other mechanisms, including geographic distance and population dynamics, shape genetic variation. Pecan is an ecologically, culturally, and economically important North American tree, and a broader understanding of the genetics of environment adaptation will aid pecan conservation, breeding, and commercial management. Here, we use an expansive set of more than 700 pecan genotypes in combination with the first haplotype-resolved genome assembly for pecan to assess species-wide genetic variation and evaluate environmental adaptation across the native distribution. We identify five gene pools in pecan, with the lowest diversity in southern gene pools, and present evidence that gene pools began differentiating during multiple glacial cycles. Using complementary genotype-environment association approaches, we infer species-wide patterns of environmental adaptation. With these results, we predict mismatches in adaptation for pecan genotypes to different environments, including future environment scenarios. We see that in all locations, present-day genotypes incur some level of predicted maladaptation to simulated future environments, but current genetic diversity may provide a valuable source of resilience to future conditions through assisted migration. These results expand the understanding of environmental adaptation in pecan and provide insight into how long-lived species will be able to adapt to future conditions.

evolutionary biology↗

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

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

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

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

A haplotype-resolved reference genome for Eucalyptus grandis

E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al., 2015; Myburg et al., 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species. Paper summaryWe assembled a haplotype-phased genome for Eucalyptus grandis that will serve as reference for the most widely planted hardwood crop globally. It includes more than 430 new gene models with long introns and has 6% higher annotation completeness. The phased assembly provides a more accurate look at genome variation at DNA and transcript level and will better support future studies of genome structure and function. The improved assembly contains more tandem duplicate genes compared to the previous unphased reference. Finally, major genomic rearrangements between the two phased genomes provide a preview of pangenome and structural variation in E. grandis.

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↗