Genomic Relationships of Glycine remota, a Recently Discovered Perennial Relative of Soybean, within Glycine

Abstract

Abstract— The legume genus, Glycine, which includes the Asian annual cultivated soybean, also includes a group of Australian perennial species comprising the subgenus Glycine. Because the subgenus Glycine represents the tertiary gene pool for one of the world’s most important crops, the group has been the target of collection and study for decades, resulting in a steady growth in the number of formally recognized species, from six in the 1970s to over 20 at present, as well as a number of additional informal taxa. These studies have also produced a system of nuclear diploid “genome groups” corresponding to clades in molecular phylogenies. The aptly named G. remota is known only from a single isolated population in the Kimberley region of northwestern Australia and was named only in 2015. The species is unique within Glycine in having unifoliolate leaves; its discoverers hypothesized that G. remota, if diploid, is related to species of the I-genome that are also native to the Kimberley region. We produced low coverage short-read genome sequencing data from an herbarium specimen of G. remota. Genome size estimates from the sequencing data suggests that G. remota is a diploid, while ploidy estimation is inconclusive likely due to the history of whole genome duplication in Glycine. Phylogenomic analyses of genome-wide SNPs, as well as phylogenetic analyses of the low copy nuclear gene (histone H3D), the entire ribosomal RNA cistron, and the internal transcribed spacer all placed the species unequivocally in the diploid I-genome clade. A complete plastome sequence was also generated and its placement with a plastome phylogeny is also consistent with membership in the I-genome.