Identification and Bioinformatics Analysis of the bHLH Transcription Factor Family in Cucurbita moschata Duch.

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

Abstract

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

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.

Figures/Tables 7

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

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.

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

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

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

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

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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