Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae.

KEY MESSAGE: Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86-77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.