Comparative Analyses of 18 Complete Chloroplast Genomes from Eleven Mangifera Species (Anacardiaceae): Sequence Characteristics and Phylogenomics

Abstract

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly sequenced chloroplast genomes as well as six existing genomes obtained from the National Center for Biotechnology Information (NCBI) database. The chloroplast genomes all had a typical quadripartite structure, with lengths ranging from 157,368 to 158,942 bp. The GC-content in the genomes ranged from 37.8% to 37.9%. We found conserved boundaries comprised of two inverted repeats (IRs), large single-copy (LSC) regions, and small single-copy (SSC) regions. Nucleotide polymorphism analysis revealed three hypervariable regions (ycf4-cemA, rps18-rpl20, and rpl32-ndhF) in the LSC and SSC regions, which could potentially be used as DNA barcodes for Mangifera species. According to our phylogenetic analysis, Mangifera plants were clustered into three clades. Among them, all five samples of M. indica formed a monophyletic group in Clade Ⅰ. Clade Ⅱ included seven Mangifera species and could be further divided into five subclades with 100% branch support values. Clade Ⅲ included two M. persiciforma samples that formed a monophyletic group. Taken together, these results provide a theoretical basis for species determination, in addition to shedding light on the evolution of Mangifera.