Rice species and their phylogenetic relationships
The phylogenetic relationships among Oryza species were reconstructed based on their complete chloroplast genomes, as well as the nuclear ITS, NP78, and R22 genes. The eight clades in the complete chloroplast genome phylogeny matched exactly the eight genome types (Fig. 1). The species O. malampuzhaensis and O. minuta of the BC genome type formed a clade with O. punctata , indicating that a species of the B genome type was their maternal parent. O. alta , O. grandiglumis , and O. latifolia of the CD genome type and O. schweinfurthianaof the BC genome type formed a clade with species of theC genome type, suggesting their maternal parent belonged to theC genome type. Species with HJ and HK genome types did not form monophyletic clades, indicating that a species of theH genome type was their paternal parent.
Phylogeny based on nuclear genes clarified the origins of allotetraploid species. Haplotypes of the same genome types formed monophyletic clades (Fig. 2). The clade comprising species with F and Ggenome types was located at the base, consistent with Fig. 1. TheH haplotypes formed a clade independent of clades Jand K , suggesting that a paternal parent with the Hgenome type had existed but then died out. The D haplotypes formed a clade with E haplotypes, indicating that theD genome type is a form of E . The species with aBC genome had independent origins, with O. malampuzhaensis = O. officinalis (C ) × O. punctata (B ) and O. schweinfurthiana = O. punctata (B ) × O. eichingeri (C ).
Genetic divergence between species of the same genome type was rather small, except between O. schlechteri and O. coarctata . No significant chloroplast genome divergence was observed between O. alta and O. grandiglumis , or between O. barthii andO. glaberrima . Minor divergence was detected between O. glumipatula and O. longistaminata . In contrast, chloroplast genome divergence was clearly noted between O. sativa subsp.indica and subsp. japonica . The former formed a monophyletic clade with O. nivara , and the latter formed a monophyletic clade with O. rufipogon .