Comparative analysis of complete chloroplast genome sequences and insertion-deletion (Indel) polymorphisms to distinguish five Vaccinium species

Abstract

We report the identification of interspecific barcoding InDel regions in Vaccinium species. We compared five complete Vaccinium chloroplast (cp) genomes (V. bracteatum, V. vitis-idaea, V. uliginosum, V. macrocarpon, and V. oldhamii) to identify regions that can be used to distinguish them. Comparative analysis of nucleotide diversity from five cp genomes revealed 25 hotspot coding and noncoding regions, occurring in 65 of a total of 505 sliding windows, that exhibited nucleotide diversity (Pi) > 0.02. PCR validation of 12 hypervariable InDel regions identified seven candidate barcodes with high discriminatory powers: accD-trnT-GGU, rpoB-rpoA, ycf2-trnL-GAA, rps12-ycf15, trnV-GAC, and ndhE-ndhF. Among them, the rpoB-rpoA(2) and ycf2-trnL-CAA sequences clearly showed the intraspecific and interspecific distance among five Vaccinium species by using a K2P technique. In phylogenetic analysis, included five Vaccinium species (n = 19) in the Bayesian and Neighbor-Joining (NJ) analysis revered all species in two major clades and resolved taxonomic position within species groups. These two locus provide comprehensive information that aids the phylogenetics of this genus and increased discriminatory capacity during species authentication.