Table_3_Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications.XLSX

Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI–atpA, atpH–atpI, rpoB–petN, psbM–psbD, ndhf–rpl32, and ndhG–ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.

芭蕉属（Musa，芭蕉科（Musaceae））为隶属于姜目（Zingiberales）的单子叶植物，多生长于热带与亚热带区域，是全球至关重要的热带果树之一。本研究首次借助下一代测序技术，完成了9株全新芭蕉属材料的叶绿体基因组组装与深度解析，分析内容涵盖基因组结构、GC含量、重复序列结构、密码子使用偏好性、核苷酸多样性等多个方面。芭蕉属叶绿体基因组的全长介于167975 bp至172653 bp之间，共包含113个独特基因，其中79个为蛋白质编码基因、30个转运RNA（tRNA）基因以及4个核糖体RNA（rRNA）基因。比较基因组分析结果显示，反向重复（inverted repeat, IR）区域的收缩与扩张事件，导致rps19基因发生了拷贝倍增。多个非编码位点（psbI–atpA、atpH–atpI、rpoB–petN、psbM–psbD、ndhf–rpl32及ndhG–ndhI）以及3个基因（ycf1、ycf2与accD）呈现出显著的序列变异，表明这些位点与基因具备开发为分子标记的潜力。基于完整叶绿体基因组与77个蛋白质编码基因的编码序列开展的系统发育分析证实，芭蕉属植物可被划分为两个主要演化支。上述基因组序列为芭蕉属植物资源的开发与利用提供了重要的分子基础，本研究结果有助于深化对芭蕉属植物演化模式、系统发育关系以及分类学的认知。