Cercis: A non-polyploid genomic relic within the generally polyploid legume family

Authors: STAI, JACOB - Iowa State University; YADAV, AKSHAY - Iowa State University; SINOU, CAROLE - University Of Montreal; BRUNEAU, ANNE - University Of Montreal; DOYLE, JEFF - Cornell University; FERNANDEZ-BACA, DAVID - Iowa State University; Cannon, Steven

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2019
Publication Date: 4/11/2019
Citation: Stai, J.S., Yadav, A., Sinou, C., Bruneau, A., Doyle, J.J., Fernandez-Baca, D., Cannon, S.B. 2019. Cercis: A non-polyploid genomic relic within the generally polyploid legume family. Frontiers in Plant Science. 10:345. https://doi.org/10.3389/fpls.2019.00345.
DOI: https://doi.org/10.3389/fpls.2019.00345

Interpretive Summary: The large legume plant family includes more than two dozen diverse crops, such as peanut, soybean, lentil, and pea, as well as less-widely known crops such as jicama, lupin, and tamarind. Efficient breeding in these crops requires development of genetic markers associated with traits such as seed size and time to maturity - which in turn requires identifying where those traits are located in the chromosomes of each species. Those traits are often controlled by genetic elements that have common evolutionary histories and can be traced to corresponding chromosome locations. Understanding the evolutionary histories and chromosomal correspondences is therefore important both for discovering the genetic control of traits, and for identifying related genetic markers that can be used in numerous species. The research in this paper presents a model of the evolution of all legume species, presenting evidence that all but one small group of species in this large family experienced an early whole-genome duplication (doubling of all chromosomes). The few species that lack this duplication, including the redbud tree (Cercis canadensis), appear to have simpler and smaller genomes than all other legume species, and can therefore serve as a useful guide and reference for the many other agronomically legume important crops. This basic knowledge will be useful to plant researchers and breeders, for relating and extending knowledge about chromosome evolution in this plant family, ultimately enabling more efficient breeding strategies for many crops.

Technical Abstract: Based on genome sequences for more than a dozen diverse legume species, we conclude that there is a plausible model for the “ur-legume genome” in the genus Cercis. The genome of Cercis canadensis lacks evidence for any polyploidy events known or hypothesized to have occurred within legumes. Earlier reports indicate that a duplication occurred early in the Caesalpinioideae clade, and another is inferred just preceding the Papilionoid radiation. We also infer an early duplication within the Cercidoideae – though not affecting Cercis itself. There is evidence for a genome duplication in the remaining Cercidoideae, which we argue is likely due to allotetraploidy involving a Cercis progenitor and a diploid species that existed at the time of the polyploidy event. Examining other genome assemblies and gene families, we conclude that most (perhaps all) other legume species have a history of polyploidy.