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<p>Banana (<i>Musa</i> spp.) is a critical staple crop with a complex domestication history involving interspecific hybridization between <i>Musa acuminata</i> (A-genome) and <i>Musa balbisiana</i> (B-genome) progenitors. Despite Malaysia’s role as a major centre of origin and domestication, chloroplast genomic resources for Malaysian cultivated varieties remain underrepresented in public databases. We sequenced and assembled the complete chloroplast genomes of two commercially important Malaysian accessions, <i>Musa acuminata</i> cv. Berangan and <i>Musa balbisiana</i> cv. Nipah. Genome features, repeat organization, and codon usage were characterized. The chloroplast genomes measured 170,035&#xa0;bp (<i>M. acuminata</i> cv. Berangan) and 170,308&#xa0;bp (<i>M. balbisiana</i> cv. Nipah), both exhibiting the typical quadripartite structure. Both genomes contained 113 genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and 4 ribosomal RNA (rRNA) genes. Both cultivars displayed strong A/U-ending codon usage bias. A total of 76 and 92 simple sequence repeats (SSRs) were identified. Long repeat content was higher in <i>M. balbisiana</i> cv. Nipah (664 repeats) than in <i>M. acuminata</i> cv. Berangan (331 repeats). Nucleotide diversity analysis identified several hypervariable regions including <i>ndhF</i>, <i>ycf1</i> and intergenic spacers. IR expansion resulted in duplication of the <i>ycf1, rps15, ndhH</i> and <i>ndhA</i> genes in both accessions. High sequence divergence was revealed in intergenic spacer regions (<i>psbI-atpA, atpH-atpI</i> and <i>rpl23-ycf2</i>) and in coding regions <i>accD</i>, <i>ycf1</i>, <i>ycf2</i> and <i>ndhF.</i> Phylogenetic analysis resolved <i>M. acuminata</i> cv. Berangan within the <i>M. acuminata</i> subspecies clade, clustering closely with <i>M. acuminata</i> subsp. <i>zebrina</i>. Whereas <i>M. balbisiana</i> cv. Nipah clustered with <i>M</i>. <i>balbisiana</i> consistent with maternal inheritance in both accessions<i>.</i> These findings provide a molecular foundation for the conservation, molecular breeding and understanding of banana domestication in Southeast Asia.</p>

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

  • 期刊论文

  • 发表日期：

    2026年5月25日

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  • Maria Ulfa Md Shah,
  • Rofina Yasmin Othman,
  • Sze-Looi Song,
  • Jennifer Ann Harikrishna,
  • Yusmin Mohd-Yusuf

摘要

Banana (Musa spp.) is a critical staple crop with a 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 underrepresented in public databases. We sequenced and assembled the complete chloroplast genomes of two commercially important Malaysian accessions, Musa acuminata cv. Berangan and Musa balbisiana cv. Nipah. Genome features, 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 contained 113 genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and 4 ribosomal RNA (rRNA) genes. Both cultivars displayed strong A/U-ending codon usage bias. A total of 76 and 92 simple sequence repeats (SSRs) were identified. Long repeat content was higher in M. balbisiana cv. Nipah (664 repeats) than in M. acuminata cv. Berangan (331 repeats). Nucleotide diversity analysis identified several hypervariable regions including ndhF, ycf1 and intergenic spacers. IR expansion resulted in duplication of the ycf1, rps15, ndhH and ndhA genes in both accessions. High sequence divergence was revealed in intergenic spacer regions (psbI-atpA, atpH-atpI and rpl23-ycf2) and in coding regions accD, ycf1, ycf2 and ndhF. Phylogenetic analysis resolved M. acuminata cv. Berangan within the M. acuminata subspecies clade, clustering closely with M. acuminata subsp. zebrina. Whereas M. balbisiana cv. Nipah clustered with M. balbisiana consistent with maternal inheritance in both accessions. These findings provide a molecular foundation for the conservation, molecular breeding and understanding of banana domestication in Southeast Asia.