Characteristics of the Complete Chloroplast Genome of Pourthiaea (Rosaceae) and Its Comparative Analysis

Abstract

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159–160,401 bp, in which the large single copy was 88,047–88,359 bp, the small single copy was 19,234–19,338 bp, and the lengths of a pair of inverted repeats were 26,341–26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi > 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea.