Data_Sheet_1_Genome-Wide Analysis of Basic Helix-Loop-Helix Transcription Factors to Elucidate Candidate Genes Related to Fruit Ripening and Stress in Banana (Musa acuminata L. AAA Group, cv. Cavendish).xlsx

The basic helix−loop−helix (bHLH) proteins are a superfamily of transcription factors (TFs) that can bind to specific DNA target sites, playing a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, no systemic analysis of bHLH TFs has been reported in banana, a typical climacteric fruit in tropical and subtropical regions. In our study, 259 MabHLH TF genes were identified in the genome of Musa acuminata (A genome), and phylogenetic analysis indicated that these MabHLHs could be classified into 23 subfamilies with the bHLHs from rice and Arabidopsis. The amino acid sequences of the bHLH domain in all MabHLH protein sequences were quite conserved, especially Arg-12, Arg-13, Leu-23, and Leu-79. Distribution mapping results showed that 258 MabHLHs were localized on the 11 chromosomes in the M. acuminata genome. The results indicated that 40.7% of gene duplication events were located in collinear fragments, and segmental duplications might have played a key role in the expansion of MabHLHs. Moreover, the expression profiles of MabHLHs in different fruit development and ripening stages and under various abiotic and biotic stresses were investigated using available RNA-sequencing data to obtain fruit development, ripening-specific, and stress-responsive candidate genes. Finally, a co-expression network of MabHLHs was constructed by weighted gene co-expression network analysis to elucidate the MabHLHs that might participate in important metabolic biosynthesis pathways in banana during development and the response to stress. A total of 259 MabHLHs were identified, and their sequence features, conserved domains, phylogenetic relationships, chromosomal distributions, gene duplications, expression profiles, and co-expression networks were investigated. This study systematically identified the MabHLHs in the M. acuminata genome at the genome-wide level, providing important candidate genes for further functional analysis. These findings improve our understanding of the molecular basis of developmental and stress tolerance in an important banana cultivar.

碱性螺旋-环-螺旋（basic helix-loop-helix, bHLH）蛋白是一类可结合特定DNA靶位点的转录因子（transcription factors, TFs）超家族，在高等生物的广泛代谢、生理及发育过程中发挥核心作用。然而，针对热带与亚热带地区典型跃变型果实香蕉的bHLH转录因子，目前尚无系统性分析研究报道。本研究从小果野蕉（Musa acuminata，A基因组）的基因组中鉴定出259个MabHLH转录因子基因；结合水稻与拟南芥的bHLH蛋白进行系统发育分析后发现，这些MabHLH蛋白可划分为23个亚家族。所有MabHLH蛋白序列中的bHLH结构域氨基酸序列均较为保守，尤其是精氨酸-12（Arg-12）、精氨酸-13（Arg-13）、亮氨酸-23（Leu-23）与亮氨酸-79（Leu-79）。染色体分布定位结果显示，258个MabHLH基因定位于小果野蕉基因组的11条染色体上。研究结果表明，40.7%的基因复制事件位于共线性片段中，片段复制可能在MabHLH基因家族的扩张过程中发挥关键作用。此外，本研究利用现有RNA测序（RNA-sequencing）数据，对MabHLH基因在不同果实发育与成熟阶段以及多种非生物、生物胁迫下的表达谱进行分析，以筛选获得与果实发育、成熟特异性相关以及响应胁迫的候选基因。最后，通过加权基因共表达网络分析构建MabHLH基因的共表达网络，以阐明可能参与香蕉发育及胁迫响应过程中重要代谢生物合成途径的MabHLH成员。本研究共鉴定出259个MabHLH基因，并对其序列特征、保守结构域、系统发育关系、染色体定位、基因复制模式、表达谱及共表达网络进行了系统性研究。本研究在全基因组水平上系统性鉴定了小果野蕉基因组中的MabHLH基因家族，为后续功能分析提供了重要的候选基因。上述研究结果有助于加深我们对重要香蕉栽培品种发育与胁迫耐受性分子基础的理解。