Abstract
BackgroundLimited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus.ResultsThe results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya.ConclusionOur results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time.
Highlights
Amygdalus L. (Rosaceae), a subgenus of the genus Prunus L. [1,2,3], is a small group within Prunus that includes approximately 24 species
Amygdalus species exhibited a circular DNA molecule with a typical quadripartite structure; they have a pair of inverted repeats regions (IRa and IRb), one large single-copy (LSC) region, and one small single-copy (SSC) region (Fig. 1, Table 1)
Amygdalus species ranged from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana) in length
Summary
Amygdalus L. (Rosaceae), a subgenus of the genus Prunus L. [1,2,3], is a small group within Prunus that includes approximately 24 species. [1,2,3], is a small group within Prunus that includes approximately 24 species. Amygdalus members are shrubs or small trees that mostly grow between 1000 and 2500 m above sea level in mountainous areas [5]. Amygdalus species are valuable fruit trees and can be common ornamental plants, among which P. persica has over one thousand years of cultural history and is one of the five. Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg.
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