The complete chloroplast genome sequence of Oryza rhizomatis (Poaceae)

The complete chloroplast genome sequence of Oryza rhizomatis (GenBank accession number: KX085497) was generated by de novo assembly with low-coverage whole-genome sequence data. The genome was 134,796 bp in length, containing a pair of inverted repeat (IRa and IRb) regions of 20,818 bp, which were separated by a large single-copy (LSC) region of 80,829 bp and a small single-copy (SSC) region of 12,330 bp, respectively. The genic regions account for 43.77% of whole cpDNA, and the AT content of the cpDNA was 60.99%. The O. rhizomatis cpDNA encodes 112 unigenes (79 protein-coding genes, four rRNA genes, and 29 tRNA genes). Eighteen genes contain introns, ycf3 contains two introns, and the rest of the gene contains one intron; rps12 is trans-spliced, one of its exons is in the LSC region (5'_end) and the two reside in the IR regions (3'_end) separated. A pair of gene ndhH, due to the 5' part of ndhH which overlaps the IR/SSC junctions, was two unique genes. The four rRNA genes are all located in the IR. Phylogenomic analysis showed that O. rhizomatis is closely related to O. officinalis. The new data will help to determine the phylogenetic placement of the genus Oryza and fill gaps in our understanding of Oryzae biology.