Characterization and Phylogenetic Analysis of the Complete Chloroplast Genome of Orinus kokonoricus (Poaceae), an Endemic Species from the Qinghai-Tibet Plateau

Abstract

Orinus kokonoricus is an alpine perennial grass (Poaceae) endemic to the Qinghai-Tibet Plateau (QTP) in China, which has extremely important ecological and genetic values. To explore characterization and phylogenetic analysis of the complete chloroplast (cp) genome of O. kokonoricus, we first sequenced and assembled its cp genome with Illumina HiSeq4000 platform in the present study. The results showed that the complete cp genome of O. kokonoricus is 134,466 bp in length with a high AT content of 61.6% and displays a standard quadripartite structure including one large single copy region (LSC, 79,932 bp), one small single copy region (SSC, 12,490 bp) and two inverted repeat regions (IRA and IRB, 21,022 bp each). It totally encodes 137 genes containing 81 protein-coding genes, 45 tRNAs genes and eight rRNAs genes. Moreover, most of these genes occur in the single copy regions. Among all annotated genes of the cp genome of O. kokonoricus, none of them harbors introns. In addition, phylogenetic analysis based on 40 complete cp genome sequences of Poaceae revealed that O. kokonoricus is sister clade to the clade of Eragrostis species in Chloridoideae.