Structure and sequence evolution in the pennycress ( <i>Thlaspi arvense</i> ) pangenome
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.
Authors
- Patrick P. Edger (ORCID: https://orcid.org/0000-0001-6836-3041)
- Kathleen Greenham (ORCID: https://orcid.org/0000-0001-7681-5263)
- Shanmugam Rajasekar (ORCID: https://orcid.org/0000-0001-9038-5618)
- LoriBeth Boston
- Kerrie Barry (ORCID: https://orcid.org/0000-0002-8999-6785)
- Jayson Talag (ORCID: https://orcid.org/0000-0001-6085-214X)
- Kevin A. Bird (ORCID: https://orcid.org/0000-0002-3174-3646)
- Anna Lipzen (ORCID: https://orcid.org/0000-0003-2293-9329)
- Rachel Walstead (ORCID: https://orcid.org/0000-0002-4372-2703)
- Jie Guo (ORCID: https://orcid.org/0000-0003-2268-7926)
- Katherine Frels (ORCID: https://orcid.org/0000-0003-3032-5570)
- Ella Katz (ORCID: https://orcid.org/0000-0003-1619-5597)
- Avril M. Harder (ORCID: https://orcid.org/0000-0001-7371-4002)
- Pawan Basnet (ORCID: https://orcid.org/0000-0001-5496-9165)
- Daniel J. Kliebenstein (ORCID: https://orcid.org/0000-0001-5759-3175)
- Christopher Plott (ORCID: https://orcid.org/0000-0002-0109-5174)
- Chloee M. McLaughlin (ORCID: https://orcid.org/0000-0002-6345-6764)
- Shelby Ellison (ORCID: https://orcid.org/0000-0002-0790-4286)
- Tomáš Brůna (ORCID: https://orcid.org/0000-0001-9811-5532)
- Joanna L. Rifkin (ORCID: https://orcid.org/0000-0003-1980-5557)
- John T. Lovell
- J. Chris Pires
- Jane Grimwood
- Jerry W. Jenkins
- Christopher Daum
- Jeremy Schmutz
Institutions
- University of Nebraska–Lincoln (US)
- Translational Genomics Research Institute (US)
- University of Minnesota (US)
- University of Wisconsin–Madison (US)
- University of Arizona (US)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- Royal Botanic Gardens, Kew (GB)
- HudsonAlpha Institute for Biotechnology (US)
- University of California, Davis (US)
- Michigan State University (US)
- Colorado State University (US)
Publication Details
- Journal
- New Phytologist
- Published
- 2026-04-02
- DOI
- https://doi.org/10.1111/nph.71111
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Joint Genome Institute
- National Institute of Food and Agriculture
- Division of Molecular and Cellular Biosciences
- Division of Integrative Organismal Systems