Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species

Authors: REN, LONGHUI - Iowa State University; HUANG, WEI - Iowa State University; Cannon, Steven

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2019
Publication Date: 3/4/2019
Citation: Ren, L., Huang, W., Cannon, S.B. 2019. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. New Phytologist. https://doi.org/10.1111/nph.15770.
DOI: https://doi.org/10.1111/nph.15770

Interpretive Summary: Many species in the legume family are important crops, including soybean, pea, lentil, common bean, peanut, alfalfa. Because these species shared a common ancestor within a few tens of millions of years, it is often possible to use information from one of these species to guide the breeding choices in the other species - for example, by selecting genetic markers that can be used in a breeding program. This cross-species transfer of information is aided by having a clear picture of the changes that have occurred in the chromosomes of these species over evolutionary time. This paper describes a model of the evolutionary history of the chromosomes of crop legumes, including a reconstruction of common ancestor of these species, in terms of the order of the ancestral genes from the common progenitor species. The model (or hypothesis) is of an ancestor with nine chromosomes, approximately 50 million years ago, which diverged and evolved to produce the many crop legume species now used by humans - species with chromosome numbers that vary in number from seven (lentil) to 20 (soybean and peanut). This model of the evolutionary history of these crops will help researchers and breeders more efficiently identify useful genetic markers that can be used for breeding projects in many important species.

Technical Abstract: Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole genome duplications (WGDs), segmental duplications, independent gene duplications or losses, diploidization, and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome for the papilionoid legumes (the largest subfamily within the third largest family in flowering plants), and evaluate the results relative to phylogenetic and chromosomal count data for this group of legumes, spanning 294 diverse papilionoid genera. To reconstruct the ancestral genomes for nine legume species with sequenced genomes, we used a maximum likelihood approach combined with a novel method for identifying informative markers for this purpose. Analyzing genomes from four species within the Phaseoleae, two in Dalbergieae, two in the IRLC clade, and one in the Robineae, we infer a common ancestral genome with 9 chromosomes. The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories – but we also infer that a common ancestor with 9 chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole-genome duplication that predated the radiation of the papilionoid legumes – evidence for which is found in a set of early-diverging papilionoid lineages.