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

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, 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 'inverted repeat loss' clade, and one in the Robinieae, we infer a common ancestral genome with nine chromosomes. The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories, but we also infer that a common ancestor with nine chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole-genome duplication that pre-dated the radiation of the papilionoid legumes, evidence for which is found in early-diverging papilionoid lineages.