Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

Authors: LEE, HYUN-OH - Oak Ridge Institute For Science And Education (ORISE); STAI, JACOB - Oak Ridge Institute For Science And Education (ORISE); XU, QIAOJI - University Of Ottawa; HEWAVITHANA, THULANI - University Of Saskatchewan; SOMAN, PRATHEESH - University Of Saskatchewan; BATRA, RABNOOR - University Of Saskatchewan; LIU, ALEX - University Of Waterloo; Jordan, Brandon; WALSTEAD, RACHEL - Hudsonalpha Institute For Biotechnology; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; WILLIAMS, MELISSA - Hudsonalpha Institute For Biotechnology; WEBBER, JENELL - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; LOVELL, JOHN - Hudsonalpha Institute For Biotechnology; BRUNA, TOMÁŠ - Department Of Energy Joint Genome; SHU, SHENGQIANG - Department Of Energy Joint Genome; KEYMANESH, KEYKHOSROW - Department Of Energy Joint Genome; EICHENBERGER, JOANNE - Department Of Energy Joint Genome; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; GOODSTEIN, DAVID - Department Of Energy Joint Genome; BARRY, KERRIE - Department Of Energy Joint Genome; SANKOFF, DAVID - University Of Ottawa; JIN, LINGLING - University Of Saskatchewan; LEEBENS-MACK, JAMES - University Of Georgia; Cannon, Steven

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2026
Publication Date: 6/10/2026
Citation: Lee, H., Stai, J.S., Xu, Q., Hewavithana, T., Soman, P., Batra, R., Liu, A., Jordan, B.D., Walstead, R., Jenkins, J., Williams, M., Webber, J., Grimwood, J., Lovell, J.T., Bruna, T., Shu, S., Keymanesh, K., Eichenberger, J., Schmutz, J., Goodstein, D.M., Barry, K., Sankoff, D., Jin, L., Leebens-Mack, J.H., Cannon, S.B. 2026. Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes. The Plant Journal. https://doi.org/10.1111/tpj.70981.
DOI: https://doi.org/10.1111/tpj.70981

Interpretive Summary: 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 ' 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.

Technical Abstract: The legume family originated ca. 70 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. This study reports the genome sequences and annotations for Cercis canadensis (Cercidoideae) and Chamaecrista fasciculata (Caesalpinoideae) to help resolve the relative taxonomic placements along the legume backbone, 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. Our analysis supports an allopolyploid origin of the subfamily Caesalpinoideae, with progenitors involving lineages along the backbone of the legume phylogeny. A probable allopolyploid origin of Caesalpinoideae subfamily provides a partial explanation for the difficulty in resolving the structure of the legume backbone. The retained karyotype structure and lack of a WGD in the last 100+ Mya, underscore the utility of the Cercis genome as an ancestral reference for the legume family.