Dataset Information

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.).

ABSTRACT: Plant basic helix-loop-helix (bHLH) transcription factors are involved in the regulation of various biological processes in plant growth, development, and stress response. However, members of this important transcription factor family have not been systematically identified and analyzed in pepper (Capsicum annuum L.). In this study, we identified 122 CabHLH genes in the pepper genome and renamed them based on their chromosomal locations. CabHLHs were divided into 21 subfamilies according to their phylogenetic relationships, and genes from the same subfamily had similar motif compositions and gene structures. Sixteen pairs of tandem and segmental duplicated genes were detected in the CabHLH family. Cis-elements identification and expression analysis of the CabHLHs revealed that they may be involved in plant development and stress responses. This study is the first comprehensive analysis of the CabHLH genes and will serve as a reference for further characterization of their molecular functions.

SUBMITTER: Zhang Z

PROVIDER: S-EPMC7545091 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.).

Zhang Zhishuo Z Chen Juan J Liang Chengliang C Liu Feng F Hou Xilin X Zou Xuexiao X

Frontiers in genetics 20200925

Plant basic helix-loop-helix (bHLH) transcription factors are involved in the regulation of various biological processes in plant growth, development, and stress response. However, members of this important transcription factor family have not been systematically identified and analyzed in pepper (Capsicum annuum L.). In this study, we identified 122 CabHLH genes in the pepper genome and renamed them based on their chromosomal locations. CabHLHs were divided into 21 subfamil ...[more]

PMID: 33101390

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Project description:In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.

Dataset Information

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.).

Publications

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (<i>Capsicum annuum</i> L.).

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