DOE OSTI · 3363747
Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome
Abstract
Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies 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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Bird, Kevin A. [Royal Botanic Gardens (United Kingdom); Univ. of California, Davis, CA (United States)] (ORCID:0000000231743646), Rifkin, Joanna L. [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000319805557), McLaughlin, Chloee M. [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000263456764), Harder, Avril M. [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000173714002), Basnet, Pawan [Univ. of Wisconsin, Madison, WI (United States)] (ORCID:0000000154969165), Katz, Ella [Univ. of California, Davis, CA (United States)] (ORCID:0000000316195597), Brůna, Tomáš [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000198115532), Barry, Kerrie [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000289996785), Boston, LoriBeth [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)], Daum, Christopher [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Guo, Jie [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Lipzen, Anna [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000322939329), Plott, Christopher [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000201095174), Jenkins, Jerry W. [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000279433997), Walstead, Rachel [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000243722703), Rajasekar, Shanmugam [Univ. of Arizona, Tucson, AZ (United States). Arizona Genomics Inst.], Talag, Jayson [Univ. of Arizona, Tucson, AZ (United States). Arizona Genomics Inst.], Frels, Katherine [Univ. of Nebraska, Lincoln, NE (United States)], Greenham, Kathleen [University of Minnesota, Saint Paul, MN (United States)] (ORCID:0000000176815263), Ellison, Shelby [Univ. of Wisconsin, Madison, WI (United States)] (ORCID:0000000207904286), Grimwood, Jane [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)] (ORCID:0000000283568325), Schmutz, Jeremy [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000180629172), Edger, Patrick P. [Michigan State Univ., East Lansing, MI (United States)] (ORCID:0000000168363041), Pires, J. Chris [Colorado State Univ., Fort Collins, CO (United States)] (ORCID:0000000196822639), Lovell, John T. [HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000289381166), Kliebenstein, Daniel J. [Univ. of California, Davis, CA (United States)] (ORCID:0000000157593175). 2026-04-02. Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome. https://doi.org/10.1111/nph.71111
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