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. 2020 Mar 3;12(4):413–428. doi: 10.1093/gbe/evaa037

Fig. 1.

Fig. 1.

—Species relationships in Oryza and distribution of the O. officinalis complex. (A) Phylogenetic tree based on Oryza chloroplast sequences illustrates species relationships in the Oryza genus. Leersia perrieri is used as an outgroup. Allotetraploid species are illustrated with circles at the tips. The O. officinalis complex comprises at least ten species; most contain a C genome. The B genome diploid O. punctata is placed in the O. officinalis complex but represents a sister clade to the A genome diploid species in the Oryza sativa complex. Three species in the O. sativa complex are the progenitors of the three species/subspecies of cultivated rice, illustrated with blue arrows. Neighbor-Joining tree based on mapping Illumina short reads to the O. sativa japonica Nipponbare chloroplast genome. Bootstrap support is shown as node labels. Representative accessions were used as follows: Oryza rufipogon W1943, Oryza nivara W0106, Oryza barthii W0042, Oryza glumaepatula W1169, Oryza meridionalis W1297, Oryza longistaminata W1504, O. punctata (BB) W1514, O. minuta W1319, O. punctata schweinfurthiana (BBCC) W1564, O. officinalis W0002, O. eichingeri W1525, O. rhizomatis W1808, O. latifolia W1539, O. grandiglumis W0613, O. alta W0017, O. australiensis W0008, Oryza meyeriana W1348, Oryza granulata W0003, Oryza ridleyii W0001, Oryza longiglumis W1215, and O. brachyantha W1711. (B) Distribution of O. officinalis complex species in tropical and subtropical regions around the world. The C genome occurs in America, Africa, and Asia; the B genome occurs in Africa and Asia. The D genome is limited to American CCDD allotetraploids. The E genome only occurs in Australasia.