中国南瓜bHLH转录因子家族的鉴定与生物信息学分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0606

摘要/Abstract

摘要：

【目的】基于中国南瓜全基因组数据，鉴定中国南瓜bHLH转录因子家族成员并分析其理化性质和结构等，为中国南瓜bHLH转录因子家族的生物学功能研究提供理论支撑。【方法】利用NCBI和中国南瓜基因组数据库等对中国南瓜bHLH基因家族进行鉴定，利用ExPASy ProtParam tool、DNAMAN和MAGA5.1等软件进行基本理化性质、系统进化、保守基序、启动子作用元件和表达模式等生物信息学分析。【结果】在中国南瓜全基因组中共鉴定出153个CmobHLHs基因，不均等地分布在20条染色体上。CmobHLH蛋白质含有91-897个氨基酸，理论等电点介于4.77-10.33；亚细胞定位预测表明有139个CmobHLH蛋白位于细胞核；系统进化分析将CmobHLH蛋白分为8个亚家族；保守基序（motif）预测结果表明，中国南瓜共含10条motif，其中motif1和motif2普遍存在于153个bHLH蛋白中。CmobHLHs在中国南瓜的各个部位均有表达，CmobHLH41、CmobHLH5、CmobHLH36和CmobHLH88分别在果实、叶片、茎和根中表达量最高；盐胁迫下，100个CmobHLHs基因表达量上调，49个CmobHLHs基因表达量下调。RT-qPCR结果表明盐胁迫下CmobHLH52和CmobHLH148基因表达量显著上调，而CmobHLH8、CmobHLH83、CmobHLH93和CmobHLH115基因表达量显著下调，与转录组结果基本一致。【结论】鉴定出153个CmobHLHs基因，家族成员在不同部位和盐胁迫下的表达模式存在差异，为挖掘南瓜bHLH转录因子在抗盐等方面的功能提供理论基础。

关键词: 中国南瓜, bHLH, 理化性质, 系统进化树, 组织表达模式, 盐胁迫表达模式

Abstract:

【Objective】Based on the whole genome data of Cucurbita moschata, members of the bHLH transcription factor family in C. moschata were identified and their physicochemical properties and structural analysis were carried out, ultimately providing theoretical support for the biological function research of the bHLH transcription factor family in C. moschata.【Method】Online websites such as NCBI to identify the bHLH gene family and the tools such as the ExPASy ProtParam tool, DNAMAN, and MAGA5.1 software were used to conduct bioinformatics analysis on basic physicochemical properties, systematic evolution, conserved motifs, promoter elements, and expression patterns.【Result】The 153 CmobHLHs genes were identified in the whole genome of C. moschata, and they were unequally distributed on the 20 chromosomes of C. moschata. CmobHLH proteins contained 91-897 amino acids. Theoretical isoelectric point ranged from 4.77 to 10.33. Subcellular localization prediction showed that 139 CmobHLH proteins were located in the nucleus. Phylogenetic analysis divided 153 CmobHLH proteins into 8 subfamilies. The prediction results of motif（conservative motif）indicated that there were 10 motifs, and motif 1 and motif 2 were commonly present in 153 bHLH proteins. CmobHLHs was expressed in all parts of C. moschata, and the expressions of CmobHLH41, CmobHLH5, CmobHLH36 andCmobHLH88 were the highest in the fruits, leaves, stems and roots, respectively. Under salt stress, the expressions of 100 CmobHLHs genes were upregulated; while the expressions of 49 CmobHLHs genes were downregulated. The RT-qPCR results revealed that under salt stress, the gene expression levels of CmobHLH52 and CmobHLH148 were significantly upregulated, while the gene expression levels of CmobHLH8, CmobHLH83, CmobHLH93 and CmobHLH115 were significantly downregulated, which were consistent with the transcriptome results.【Conclusion】Total 153 CmobHLHs genes have been identified, and the expression patterns of family members vary in different parts and under salt stress, providing a theoretical basis for exploring the functions of bHLH transcription factors in salt resistance and other aspects.

Key words: Cucurbita moschata, bHLH, physical and chemical properties, systematic evolutionary tree, organizational expression pattern, expression pattern under salt stress

李彩霞, 李艺, 穆宏秀, 林俊轩, 白龙强, 孙美华, 苗妍秀. 中国南瓜bHLH转录因子家族的鉴定与生物信息学分析[J]. 生物技术通报, 2025, 41(1): 186-197.

LI Cai-xia, LI Yi, MU Hong-xiu, LIN Jun-xuan, BAI Long-qiang, SUN Mei-hua, MIAO Yan-xiu. Identification and Bioinformatics Analysis of the bHLH Transcription Factor Family in Cucurbita moschata Duch.[J]. Biotechnology Bulletin, 2025, 41(1): 186-197.

图/表 7

图1 中国南瓜中bHLH基因家族的染色体分布

Fig. 1 Chromosomal distribution of bHLH gene family in C. moschata Duch.

图2 中国南瓜bHLH家族的HLH保守结构域及分布 A：HLH保守结构域，不同位点上氨基酸字母的高度表示结构域保守性的高低；B：中国南瓜bHLH家族其他43类保守结构域的分布

Fig. 2 HLH conservative domain and distribution of bHLH family in C. moschata Duch. A: HLH conserved domain, where the height of amino acid letters at different sites indicates the level of domain conservation. B: Distribution of 43 other conserved domains of bHLH family in C. moschata Duch.

图3 中国南瓜bHLH家族的进化和结构分析 A：系统进化树；B：基因保守基序分析；C：内含子-外显子分布；内含子用黑线表示，外显子用绿色框表示；比例尺显示在底部

Fig. 3 Phylogenetic and structural analysis of the bHLH family in C. moschata Duch. A: Phylogenetic tree. B: Gene motif analysis. C: Intron and exon distribution. Introns are indicated by black lines, exons are indicated by green boxes. The scale bar is shown at the bottom

图4 中国南瓜bHLH基因家族启动子作用元件分析

Fig. 4 Analysis of promoter elements in bHLH gene family in C. moschata Duch.

图5 中国南瓜bHLH基因家族组织表达分析 F、L、S、R分别代表果、叶、茎、根

Fig. 5 Tissue expression analysis of bHLH gene family in C. moschata Duch. F, L, S, and R indicate fruits, leaves, stems, and roots, respectively

图6 中国南瓜bHLH基因家族响应盐胁迫的表达分析 “0”代表0 mmol/L NaCl;“75”代表75 mmol/L NaCl

Fig. 6 Expression analysis of bHLH gene family in response to salt stress in C. moschata Duch. “0” indicates 0 mmol/L NaCl; “75” indicates 75 mmol/L NaCl

图7 中国南瓜bHLH基因家族响应盐胁迫的RT-qPCR验证不同小写字母表示在P<0.05水平差异显著

Fig. 7 RT-qPCR validation of bHLH gene family in response to salt stress in C. moschata Duch. Different lower letters indicate significant difference at P<0.05 level

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