Complete chloroplast genome of Dongxiang wild rice and its application in phylogenetic analysis

Abstract

Complete chloroplast genome sequence is very useful for studying the evolution of species. To get chloroplast genome sequences, purification of the chloroplast or PCR amplification prior to sequencing is commonly involved in conventional approaches. Advances in DNA sequencing technology provide new opportunities to obtain chloroplast genome sequence from the whole-genome high-throughput sequencing data without purification of the chloroplast. In this study, we finished the complete chloroplast genome sequence of Dongxiang wild rice based on high-throughput sequencing data from their fresh green leaves. The chloroplast genome was 134 537 bp in size, and had a typical quadripartite structure with the large single copy (LSC, 80 585 bp) and small single copy (SSC, 12 346 bp) regions separated by two copies of an inverted repeat (IR, 20 803 bp each) region. One hundred and fifty-two chloroplast genes were successfully annotated. A phylogenetic tree was constructed based on the chloroplast genomes of Dongxiang wild rice, Indica, Japonica and 10 other genera of grasses using the neighbor-joining method. The result showed that Dongxiang wild rice had a closer relationship with Bambusa oldhamii and Panicoideae. Furthermore, the SNPs of 22 rice accessions were identified using the chloroplast genome of Dongxiang wild rice as a reference sequence and a phylogenetic tree was constructed based on these SNPs. The result illustrated that Indica had a closer relationship with wild rice-I, while Japonica was closer to wild rice-III, suggesting that Indica and Japonica were domesticated independently from different wild rice populations.

Keywords

• <italic>Oryza rufipogon</italic>
• chloroplast genome
• high-throughput sequencing
• rice domestication
• Dongxiang wild rice (China)