Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships

Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.