Chloroplast genome sequence of Begonia asteropyrifolia and comparative analysis with other related species

Begonia L. is the only species-rich genus in the Begoniaceae family, comprising more than recorded 2,000 species. However, most of the species in this genus are narrowly distributed, and the phylogenetic relationships of some Begonia sections are still unresolved. Begonia asteropyrifolia Y.M. Shui & W.H. Chen which belongs to the Begonia Sect. Coelocentrum has been listed as an endangered species in China. Due to a shortage of studies on the chloroplast genome of B. asteropyrifolia, studies of comparison and phylogeny with other related species were still scarce. Here, we sequenced the chloroplast genome of B. asteropyrifolia via the Illumina NovaSeq 6000 platform. The complete chloroplast genome of B. asteropyrifolia was 169,512 bp long with a typical circular quadripartite structure, containing a large single-copy (LSC) region (76,310 bp), a small single-copy (SSC) region (18,058 bp) and two inverted repeats (IR) regions (37,572 bp each). The chloroplast genome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The basic structure, gene content and organizations, and number of long repeats in B. asteropyrifolia are similar to previously reported congeneric species. A total of 5,759 (range 144 to 205) SSRs, 1,568 (49 each) long repeats, and 25 highly divergent regions (Pi > 0.03) were detected as candidate molecular markers for further population genetic study and species identification. Moreover, the phylogenetic analysis based on the chloroplast genomes strongly supported the division of 32 Begonia species into six groups related to geographical distribution, and the B. asteropyrifolia, Begonia ferox C.-I Peng & Yan Liu, Begonia gulongshanensis Y.M. Shui & W.H. Chen and Begonia arachnoidea C.-I Peng, Yan Liu & S.M. Ku are closely related and form one clade (Sect. Coelocentrum), which was a subclade in the Asian Clade D of Asian Begonia. Overall, the current study will be beneficial for designing new species-specific DNA markers for new species identification, evolutionary history, and conservation within Begonia.