{
  "abstract": "The legume family originated ca. 60-65 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, especially in Caesalpinioideae where the diversification and WGD signals coincide. In this study, we report the genome sequences and annotations for Cercis canadensis (Cercidoideae) and Chamaecrista fasciculata (Caesalpinioideae) to help resolve the timings of WGDs relative to subfamily origins and the ancestral legume karyotype. Analyses 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. The retained karyotype structure, the lack of a WGD in the last 100+ Mya (Cercis and the lineage leading to it following the eudicot γ whole-genome triplication), and the unusually slow rates of nucleotide substitution and structural evolution in the Cercis genome underscore its utility as a genomic proxy for the last common ancestor of all legume species. Our analysis supports an allopolyploid origin of Caesalpinioideae, with progenitors from lineages along the backbone of the legume phylogeny. Rapid diversification and the inferred allopolyploid origin of Caesalpinioideae provide a partial explanation for the difficulty in resolving the backbone of the legume phylogeny and early Caesalpinioideae diversification.",
  "abstract_shown": true,
  "affiliations": [
    "ORISE Fellow, USDA‐ARS Corn Insects and Crop Genetics Research Unit 819 Wallace Rd Ames Iowa 50011 USA",
    "Department of Mathematics University of Ottawa Ottawa Ontario K1N 6N5 Canada",
    "Department of Computer Science University of Saskatchewan Saskatoon Saskatchewan S7N 5C9 Canada",
    "School of Computer Science University of Waterloo Waterloo Ontario N2L 3G1 Canada",
    "USDA—Agricultural Research Service Corn Insects and Crop Genetics Research Unit 819 Wallace Rd Ames Iowa USA",
    "Genome Sequencing Center, HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806 USA",
    "US Department of Energy Joint Genome Institute Berkeley California 94720 USA",
    "Department of Biology University of Georgia Athens Georgia 30602 USA"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 25,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Hyun Oh Lee",
      "orcid": "0000-0001-8182-8763"
    },
    {
      "affs": [
        0
      ],
      "name": "Jacob Stai",
      "orcid": "0000-0003-4265-5657"
    },
    {
      "affs": [
        1
      ],
      "name": "Qiaoji Xu",
      "orcid": "0000-0003-3316-2172"
    },
    {
      "affs": [
        2
      ],
      "name": "Thulani M. Hewavithana",
      "orcid": "0000-0002-2579-0470"
    },
    {
      "affs": [
        2
      ],
      "name": "Pratheesh Soman",
      "orcid": "0009-0000-7263-748X"
    },
    {
      "affs": [
        2
      ],
      "name": "Rabnoor Batra",
      "orcid": "0009-0004-9805-2024"
    },
    {
      "affs": [
        3
      ],
      "name": "Alex Liu",
      "orcid": "0009-0009-8963-4563"
    },
    {
      "affs": [
        4
      ],
      "name": "Brandon D. Jordan",
      "orcid": "0009-0001-0670-6165"
    },
    {
      "affs": [
        5
      ],
      "name": "Rachel Walstead",
      "orcid": "0000-0002-4372-2703"
    },
    {
      "affs": [
        5
      ],
      "name": "Jerry W. Jenkins",
      "orcid": "0000-0002-7943-3997"
    },
    {
      "affs": [
        5
      ],
      "name": "Melissa Williams"
    },
    {
      "affs": [
        5
      ],
      "name": "Jenell Webber",
      "orcid": "0009-0005-6155-6218"
    },
    {
      "affs": [
        5
      ],
      "name": "Jane Grimwood",
      "orcid": "0000-0002-8356-8325"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "John T. Lovell",
      "orcid": "0000-0002-8938-1166"
    },
    {
      "affs": [
        6
      ],
      "name": "Tomáš Brůna",
      "orcid": "0000-0001-9811-5532"
    },
    {
      "affs": [
        6
      ],
      "name": "Shengqiang Shu",
      "orcid": "0000-0002-4336-8994"
    },
    {
      "affs": [
        6
      ],
      "name": "Keykhosrow Keymanesh",
      "orcid": "0000-0001-6019-9443"
    },
    {
      "affs": [
        6
      ],
      "name": "Joanne Eichenberger"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Jeremy Schmutz",
      "orcid": "0000-0001-8062-9172"
    },
    {
      "affs": [
        6
      ],
      "name": "David M. Goodstein",
      "orcid": "0000-0001-6287-2697"
    },
    {
      "affs": [
        6
      ],
      "name": "Kerrie Barry",
      "orcid": "0000-0002-8999-6785"
    },
    {
      "affs": [
        1
      ],
      "name": "David Sankoff",
      "orcid": "0000-0001-8415-5189"
    },
    {
      "affs": [
        2
      ],
      "name": "Lingling Jin"
    },
    {
      "affs": [
        7
      ],
      "name": "Jim Leebens‐Mack",
      "orcid": "0000-0003-4811-2231"
    },
    {
      "affs": [
        4
      ],
      "name": "Steven B. Cannon",
      "orcid": "0000-0003-2777-8034"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/c8ekwk4wf8mvm.bib",
  "cited_by": 6,
  "doi": "10.1111/tpj.70981",
  "fulltext_url": null,
  "id": "c8ekwk4wf8mvm",
  "issns": [
    "0960-7412",
    "1365-313X"
  ],
  "landing_url": "https://doi.org/10.1111/tpj.70981",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1110|Chromosomal and Genetic Variations"
    ]
  ],
  "openalex": "W7164183454",
  "pdf_url": null,
  "pmcid": "PMC13252982",
  "pmid": "42269138",
  "published": "2026-06-01",
  "publisher": "Wiley",
  "ris": "https://research.draconitic.com/paper/c8ekwk4wf8mvm.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T13:20:51Z",
      "native_id": "W7164183454",
      "source": "openalex",
      "url": "https://doi.org/10.1111/tpj.70981"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1110|Chromosomal and Genetic Variations",
      "subfield": "plant-biology"
    }
  ],
  "title": "Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes",
  "title_text": "Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes",
  "type": "peer-reviewed",
  "updated_at": "2026-11-05T13:20:51Z",
  "url": "https://research.draconitic.com/paper/c8ekwk4wf8mvm",
  "venue": "The Plant Journal",
  "versions": []
}