Phylogenetic relationships in the genus Mangifera based on whole chloroplast genome and nuclear genome sequences

Abstract

The genus Mangifera (Anacardiaceae) includes 69 species with Mangifera indica L. being the most important and predominantly cultivated species for commercial mango production. Although the species are classified based on morphological descriptors, molecular evidence has proposed the hybrid origin of two species suggesting the possibility that more of the species may be of hybrid origin. To analyze evolutionary relationships within the genus, 19 samples representing 14 Mangifera species were sequenced. Whole chloroplast genomes and 47 common single-copy nuclear gene sequences were assembled and used for phylogenetic analysis using concatenation and coalescence-based methods. The chloroplast genome size varied from 151,752 to 158,965 bp with M. caesia and M. laurina having the smallest and largest genomes, respectively. Annotation revealed 80 protein-coding genes, 31 tRNA and four rRNA genes across all the species. Comparative analysis of whole chloroplast genome sequence and nuclear gene-based phylogenies revealed topological conflicts suggesting chloroplast capture or cross-hybridization. The chloroplast genomes of M. altissima, M. applanata, M. caloneura and M. lalijiwa were similar to those of M. indica (99.9% sequence similarity). Their close sequence relationship suggests a common ancestry and likely cross-hybridization between wild relatives and M. indica. This study provides improved knowledge of phylogenetic relationships in the genus Mangifera, indicating extensive gene flow among the different species, suggesting that hybridisation may be common within the genus.