Genome-wide Identification and Expression Analysis of bHLH Transcription Factor Family in Dendrobium nobile

doi:10.13560/j.cnki.biotech.bull.1985.2023-0907

Abstract

Abstract:

【Objective】 bHLH transcription factors exist widely in plants and are one of the important transcription factor families that regulate plant growth and development and respond to stress. The DnbHLHs transcription factor family was identified from the whole genome of Dendrobium nobile and its expression characteristics were analyzed, which laid the foundation for further study on the biological function of DnbHLHs transcription factor. 【Method】 The bHLH transcription factor family members were identified from the whole genome of D. nobile by bioinformatics method, and their physical and chemical characteristics, phylogenetic relationship, gene structure, chromosome localization and promoter cis-acting elements were analyzed. Transcriptome data and RT-qPCR were used to analyze the tissue expression patterns of DnbHLHs transcription factors and their expression patterns under different abiotic stresses. 【Result】 A total of 137 bHLH transcription factors were identified in D. nobile. The amino acid number of DnbHLHs protein was 85-1 260, the molecular weight was 9 855.23-140 024.19 Da, the isoelectric point was 4.52-10.66, the instability coefficient was 31.94-87.42, the fat solubility index was 56.66-106.06, and the hydrophilic index was -0.815-0.185. DnbHLHs were distributed on 19 chromosomes of D. nobile, all of which had a bHLH domain and were homologous to the bHLH of Arabidopsis thaliana, and there are collinear relationships between groups and species. Analysis of gene expression patterns showed that DnbHLHs family members had tissue specificity, and DnbHLH26 and DnbHLH33 were responsive to various stresses. 【Conclusion】 A total of 137 DnbHLHs transcription factor family members are identified from the whole genome of D. nobile. The physicochemical properties and conserved mods of the family members showe specificity and diversity. There are tissue expression differences among different DnbHLHs transcription factors, and DnbHLH26 is mainly induced by high salt and high temperature stress. DnbHLH33 is mainly induced by high salt, high temperature and low temperature stress.

Key words: Dendrobium nobile, transcription factor, bHLH, bioinformatics, expression pattern analysis

WANG Jian, YANG Sha, SUN Qing-wen, CHEN Hong-yu, YANG Tao, HUANG Yuan. Genome-wide Identification and Expression Analysis of bHLH Transcription Factor Family in Dendrobium nobile[J]. Biotechnology Bulletin, 2024, 40(6): 203-218.

Figures/Tables 13

Table 1 Primer sequences

基因 Gene	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
DnbHLH26	GGTCCTTCGCCATCTTC	CGTCAGTAACTCGGTCAA
DnbHLH33	ACGCAGTCCTTCATCAAC	GTTCATCATCTCCACACTATG
Ubiquitin	CGCCGTCAACCTCATTCCAT	GTGAGGTAGCGACCGTGGC

Fig. 1 Phylogenetic tree of bHLH family protein in D. nobile

Fig. 2 Multiple alignment of the protein sequences of D. nobile bHLH family

Fig. 3 Conserved motif prediction of bHLH transcription factor family in D. nobile

Fig. 4 Protein domain of D. nobile bHLH transcription factor family

Fig. 5 Gene structure of D. nobile bHLH transcription factor family

Fig. 6 Chromosome localization of D. nobile bHLH transcription factor family

Fig. 7 Promoter cis-acting elements of D. nobile bHLH transcription factor family members

Fig. 8 Collinearity of bHLH transcription factor family groups in D. nobile

Fig. 9 Collinear relationships among D. nobile, Arabidopsis thaliana and Oryza sativa species

Fig. 10 Expression patterns of bHLH transcription factor family in D. nobile The level represents the value of Log2（TPM+1）

Fig. 11 Tissue expression pattern analysis of bHLH transcription factors in D. nobile

Fig. 12 Analysis of expression patterns of bHLH transcription factors under stress treatment in D. nobile

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