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Summary Eukaryotic 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.Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species’s current genetic diversity to catalogue variation in genome structure and content.Across 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.Our 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.
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A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks
Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus.
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- PAR ID:
- 10581499
- Publisher / Repository:
- New Phytologist Foundation
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 246
- Issue:
- 1
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- 331-348
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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ABSTRACT Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespreadQuercus macrocarpa, we conducted a rangewide survey ofQ. macrocarpaand four sympatric eastern North American white oak species. Using a Hyb‐Seq approach, we assembled a dataset of 3412 thinned single‐nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off‐target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure withinQ. macrocarpaassociated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/nph.20463
