The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis

Abstract

Prunus triloba var. plena, also known as flowering plum, is a perennial deciduous shrub admired for its brilliant pink-purple blooms. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of P. triloba var. plena was de novo assembled with the aim of developing cp-derived molecular markers and deepening the understanding of phylogenetic relationship among Prunus species. The complete cp genome was 158,022 bp in length, with a GC content of 36.8%. The plastome featured a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26,379 bp, separated by a large single copy (LSC) region of 86,242 bp, and a small single copy (SSC) region of 19,022 bp. The cp genome encoded 134 genes, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. A total of 59 simple sequence repeat (SSR) were identified, 68% of which were located in the intergenic regions. An obvious A/T bias was observed in the majority of SSRs detected. Besides, 48 repeats in different sizes and types were detected. These repeats, together with SSRs and the divergence hotspots detected, could serve as markers facilitating species discrimination and evolutionary research in Prunus. Using plastome sequences, we re-investigated the phylogenetic relationship among 32 Prunus species. These species explicitly clustered into three monophyletic clades, among which P. triloba var. plena was closely related to species in the subgenera Amygdalus and Prunus.