Characterization of the Complete Chloroplast Genome of an Endemic Perennial Grass Orinus intermedius and Its Phylogenetic Analysis in Poaceae

Orinus intermedius is an endemic perennial species occurring exclusively in the southeastern Qinghai-Tibet Plateau (QTP). It has particularly important ecological and genetic values, and some of its morphological characters are between O. thoroldii and O. kokonoricus. In the present study, we conducted the sequencing and assembly of its complete chloroplast (cp) genome using Illumina HiSeq4000 platform in order to discuss its characterization and phylogenetic position of this species. The results showed that the complete cp genome of O. intermedius is 134 296 bp in size with a high AT content of 61.6%. The cp genome structure are standard quadripartite, which contains a pair of an inverted repeat (IRs, 21 024 bp each) separated by the small single copy (SSC, 12 478 bp) and large single copy (LSC, 79 770 bp) regions. It encodes 136 genes, including 81 protein-coding genes, 44 tRNAs genes and eight rRNAs genes. Most of these genes occur as a single copy. Moreover, there are no genes harbored introns among the annotated genes from the cp genome of O. intermedius. Phylogenetic analysis based on 41 complete cp genome sequences indicated that O. intermedius is sister clade to the clade of Eragrostis species in Chloridoideae.