Comparative Analysis and Phylogenetic Study of the Chloroplast Genome Sequences of Two Korean Endemic Primula Varieties

Abstract

Primula comprises many species of horticultural value. In Korea, six species grow in the wild. Yamazaki classified the variety Primula modesta var. fauriei into P. modesta var. hannasanensis and P. modesta var. koreana based on the differences in leaf morphology. We compared the chloroplast genome sequences of the two Korean endemic Primula varieties and found that both had the typical quadripartite structure of angiosperms. The chloroplast genome size of P. modesta var. hannasanensis is 154,772 bp, including an 85,238 bp large single-copy region and a 17,790 bp small single-copy region, whereas that of P. modesta var. koreana is 154,667 bp, including an 85,152 bp large single-copy region and a 17,771 bp small single-copy region. The inverted repeat region is 25,872 bp in both varieties. We predicted 129 genes—84 protein-coding genes, 8 rRNAs, and 37 tRNAs. We identified 536 single-nucleotide polymorphisms and 501 indels between the varieties. Phylogenetic analysis revealed that the two varieties formed a sister group in the clade P. knuthiana–P. stenocalyx. This study will contribute to phylogenetic, taxonomic, and evolutionary studies of the genus Primula; it will also contribute to the analysis of the genetic diversity of the two varieties, and to the development of identification markers.