Complete chloroplast genomes of <italic>Dioscorea opposite </italic>and <italic>D. collettii</italic> and screening specific DNA barcodes

Abstract

Previous studies of DNA barcoding Dioscorea species have shown that the identification efficiency was low. In this study, the complete chloroplast genomes of D. opposite and D. collettii were sequenced using Illumina HiSeq 2000. Genome structure and content and high variation regions were analyzed. The complete chloroplast genome lengths of D. opposite and D. collettii were 152963 and 153870 bp, which include four parts: two inverted repeats (IRs), one large single copy (LSC) and one small single copy (SSC). Both of D. opposite and D. collettii encoded 125 genes, including 87 protein coding genes, 30 tRNA genes and eight rRNA genes. The GC contents of D. opposite and D. collettii were 37.04% and 37.17%, respectively. The result showed that the sequence variation of non-coding regions is higher than that of the protein coding region and the variations of the LSC and SSC are higher than that of the IRs. Ten molecular markers of Dioscorea , which include five protein coding regions and five non-coding regions were screened to be used as the potential DNA barcodes for authenticating Dioscorea species. Phylogenetic analyses showed that the chloroplast genome can be used as an ultra-barcode to distinguish Dioscorea species from each other. This study laid the foundation for super barcode utilization in the Dioscorea and provided a molecular basis for further investigation on this important medicinal species.