Comparative analysis the complete chloroplast genomes in wild Musa species of India for its phylogenetic and taxonomic implications

The genus Musa, belonging to the family Musaceae, includes important horticultural and food crops such as bananas and plantains. In this study, we sequenced and analyzed the complete chloroplast genomes of four wild Indian Musa taxa: M. balbisiana var. andamanica, M. indandamanensis, M. paramjitiana, and M. sikkimensis, for ascertaining their taxonomic status and phylogenetic relationship. The chloroplast genomes ranged from 169,485 bp to 169,861 bp in length and exhibited a typical quadripartite structure with a pair of inverted repeat regions separated by a large single copy and a small single copy region. The genomes encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Comparative analyses revealed a relatively conserved genome structure, with coding regions being less variable than noncoding regions. Eleven divergent hotspots were identified that could serve as potential molecular markers for species identification and phylogenetic studies. Codon usage analysis revealed a preference for A/T-ending codons, and most protein-coding genes were under purifying selection. Phylogenetic analyses based on the complete chloroplast genomes and various regions (LSC, SSC, IR, and CDS) supported the conspecific status of M. paramjitiana and M. balbisiana var. andamanica with M. balbisiana. The results provide valuable insights into the evolutionary relationships and taxonomic classification of wild Musa species and highlight the potential of chloroplast genomes as tools for species identification and phylogenetic studies in the genus Musa.