Comparative Analysis of Complete Chloroplast Genome Sequences and Insertion-Deletion (Indel) Polymorphisms to Distinguish Five <i>Vaccinium</i> Species

• Main Authors: Yonguk Kim, Jawon Shin, Dool-Ri Oh, Ah-Young Kim, Chulyung Choi
• Format: Article
• Language: English
• Published: MDPI AG 2020-08-01
• Series: Forests
• Subjects: chloroplast genome; InDel; nucleotide diversity; species authentication; <i>Vaccinium</i>
• Online Access: https://www.mdpi.com/1999-4907/11/9/927

We report the identification of interspecific barcoding InDel regions in <i>Vaccinium</i> species. We compared five complete <i>Vaccinium</i> chloroplast (cp) genomes (<i>V. bracteatum</i>, <i>V. vitis-idaea</i>, <i>V. uliginosum</i>, <i>V. macrocarpon</i>, and <i>V. oldhamii</i>) 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 (<i>Pi</i>) > 0.02. PCR validation of 12 hypervariable InDel regions identified seven candidate barcodes with high discriminatory powers: <i>accD-trnT-GGU</i>, <i>rpoB-rpoA</i>, <i>ycf2-trnL-GAA</i>, <i>rps12-ycf15</i>, <i>trnV-GAC</i>, and <i>ndhE-ndhF</i>. Among them, the <i>rpoB-rpoA(2)</i> and <i>ycf2-trnL-CAA</i> sequences clearly showed the intraspecific and interspecific distance among five <i>Vaccinium</i> species by using a K2P technique. In phylogenetic analysis, included five <i>Vaccinium</i> species (<i>n</i> = 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.