Genomic relationships of Glycine remota, a recently discovered perennial relative of soybean, within the legume genus Glycine

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 suggest 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.