Complete Chloroplast Genomes of Malaysian Banana Cultivars Musa acuminata cv Berangan and Musa balbisiana cv Nipah Reveals Lineage Specific Domestication Signatures

Banana ( Musa spp.) represents a critical staple crop with complex domestication history involving interspecific hybridization between Musa acuminata (A-genome) and Musa balbisiana (B-genome) progenitors. Despite Malaysia’s role as a major centre of origin and domestication, chloroplast genomic resources for Malaysian cultivated varieties remain critically underrepresented. In this study, we sequenced and assembled chloroplast genomes of Malaysian accessions, Musa acuminata cv. Berangan and Musa balbisiana cv. Nipah. Genome features including structure, GC content, repeat organization, and codon usage were characterized. The chloroplast genomes measured 170,035 bp ( M. acuminata cv. Berangan) and 170,308 bp ( M. balbisiana cv. Nipah), both exhibiting the typical quadripartite structure. Both genomes contain 113 genes comprising 79 protein coding genes, 30 transfer RNA (tRNA) genes and 4 ribosomal RNA (rRNA) genes. A total of 76 and 92 simple sequence repeats (SSR) reported. The number of long repeats varied with 331 repeats in Musa acuminata cv. Berangan and M. balbisiana cv. Nipah and exhibited higher repeat numbers (664 repeats). Comparative analysis revealed contraction and expansion of IR regions resulting in duplication of the ycf1, rps15, ndhH and ndhA gene. Highly variable regions were detected mainly found in noncoding intergenic regions, such as in rps16-psbK, atpH-atpI, rps4-ndhJ, psbM-psbD, psbI-atpA. Divergence hotspots were detected mainly in intergenic regions, as well as coding genes such as accD , ycf1 and ycf2. Phylogenetic analysis indicated clear maternal lineage separation, M. acuminata cv. Berangan grouped with M. acuminata subspecies but closer to M. acuminata subsp. zebrina, whereas M. balbisiana cv. Nipah clustered with M . balbisiana , suggesting maternal plastid inheritance. These complete chloroplast genome sequences provide a valuable molecular foundation for the conservation, molecular breeding and understanding maternal contributions to banana domestication in Malaysia.