Phylogeny and species delimitation of the C-genome diploid species in Oryza

The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single-copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.