Development of high resolution DNA barcode for Dioscorea Species Discrimination based on chloroplast genomes. DNA barcode development in Dioscorea species

We compared genic and intergenic regions of three Dioscorea chloroplast genomes and developed 52 pairs of primers covering highly variable regions. After primer universal test, 7 pairs of primers had 80%-100% PCR success rate were selected. Moreover, Three analyzed variable regions - rpoB-trnC, psaA-ycf3 and ycf4-cemA were further estimated its applicability for species discrimination based on further sequence analysis for the seven regions. Based the genetic distance and BLAST methods, psaA-ycf3 had the highest discrimination success rate (76.5%-79.2%), followed with rpoB-trnC (70.8%-79.2%), and ycf4-cemA (69.5%-70.1%). The loci combination for the three loci has a species discrimination rate as 100% discrimination rate. We conclude that chloroplast genome sequences have provided efficient DNA bacodes and psaA-ycf3/ rpoB-trnC are strong candidate as DNA barcodes for Dioscorea.