Complete chloroplast genome of a rare and endangered plant species Osteomeles subrotunda: genomic features and phylogenetic relationships with other Rosaceae plants

Osteomeles subrotunda is a rare and endangered plant species with extremely small populations. In our study, we sequenced the complete chloroplast (CP) genome of O. subrotunda and described its structural organization, and performed comparative genomic analyses with other Rosaceae CP genomes. The plastome of O. subrotunda was 159,902 bp in length with 36.6% GC content and contained a pair of inverted repeats of 26,367 bp which separated a large single-copy region of 87,933 bp and a small single-copy region of 19,235 bp. The CP genome included 130 genes, of which 85 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Two genes, rps19 and ycf1, which are located at the borders of IRB/SSC and IRB/LSC, were presumed to be pseudogenes. A total of 61 SSRs were detected, of which, 59 loci were mono-nucleotide repeats, and two were di-nucleotide repeats. The phylogenic analysis indicated that the 14 Rosaceae species were divided into three groups, among which O. subrotunda grouped with P. rupicola, E. japonica, P. pashia, C. japonica, S. torminalis, and M. florentina, and it was found to be a sister clade to C. japonica. Our newly sequenced CP genome of O. subrotunda will provide essential data for further studies on population genetics and biodiversity.