Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis

Abstract

The sumac <i>Rhus chinensis</i> Mill. is an economically and ecologically important shrub or tree species in the family of Anacardiaceae with a wide distribution in East to Southeast Asia. We assembled the complete chloroplast genome of 159,187 bp in length and the GC content of 37.8%. The genome encoded 132 genes, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene, and 77 SSRs were identified as well as the interval regions, totaling 46,425 bp in length. The mauve alignment revealed one gene rearrangement among the <i>Rhus</i> species. All the SSRs were divided into five types, most of which consisted of mono- and tri- repeat motifs. Our genome exhibited the longest size and more annotated genes compared to the three other genomes of <i>R. chinensis</i> reported in GenBank. We also discovered some relatively highly variable regions in the complete chloroplast genomes of the <i>Rhus</i> species. The ML phylogenetic analysis of the available chloroplast sequences of the Anacardiaceae well supported the monophyly of each tribe and each genus; the tribe Rhoideae was close to the tribe Anacardiaceae with a high support of 100%, and they then grouped with the tribe Spondiadeae. <i>R. chinensis</i> was sister to <i>R. potaninii</i>, and they then grouped with the species <i>R. typhina</i>.