Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes
8 affiliations
- 1ORISE Fellow, USDA‐ARS Corn Insects and Crop Genetics Research Unit 819 Wallace Rd Ames Iowa 50011 USA
- 2Department of Mathematics University of Ottawa Ottawa Ontario K1N 6N5 Canada
- 3Department of Computer Science University of Saskatchewan Saskatoon Saskatchewan S7N 5C9 Canada
- 4School of Computer Science University of Waterloo Waterloo Ontario N2L 3G1 Canada
- 5USDA—Agricultural Research Service Corn Insects and Crop Genetics Research Unit 819 Wallace Rd Ames Iowa USA
- 6Genome Sequencing Center, HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806 USA
- 7US Department of Energy Joint Genome Institute Berkeley California 94720 USA
- 8Department of Biology University of Georgia Athens Georgia 30602 USA
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.
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BibTeX
@article{lee2026legume,
title = {{Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes}},
author = {Hyun Oh Lee and Jacob Stai and Qiaoji Xu and Thulani M. Hewavithana and Pratheesh Soman and Rabnoor Batra and Alex Liu and Brandon D. Jordan and Rachel Walstead and Jerry W. Jenkins and Melissa Williams and Jenell Webber and Jane Grimwood and John T. Lovell and Tomáš Brůna and Shengqiang Shu and Keykhosrow Keymanesh and Joanne Eichenberger and Jeremy Schmutz and David M. Goodstein and Kerrie Barry and David Sankoff and Lingling Jin and Jim Leebens‐Mack and Steven B. Cannon},
journal = {The Plant Journal},
year = {2026},
month = jun,
doi = {10.1111/tpj.70981},
url = {https://doi.org/10.1111/tpj.70981},
note = {CC BY},
}
RIS
TY - JOUR
TI - Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes
AU - Hyun Oh Lee
AU - Jacob Stai
AU - Qiaoji Xu
AU - Thulani M. Hewavithana
AU - Pratheesh Soman
AU - Rabnoor Batra
AU - Alex Liu
AU - Brandon D. Jordan
AU - Rachel Walstead
AU - Jerry W. Jenkins
AU - Melissa Williams
AU - Jenell Webber
AU - Jane Grimwood
AU - John T. Lovell
AU - Tomáš Brůna
AU - Shengqiang Shu
AU - Keykhosrow Keymanesh
AU - Joanne Eichenberger
AU - Jeremy Schmutz
AU - David M. Goodstein
AU - Kerrie Barry
AU - David Sankoff
AU - Lingling Jin
AU - Jim Leebens‐Mack
AU - Steven B. Cannon
PY - 2026
DA - 2026/06/01
JO - The Plant Journal
DO - 10.1111/tpj.70981
UR - https://doi.org/10.1111/tpj.70981
AB - 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.
SN - 0960-7412
SN - 1365-313X
ER -