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Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in c...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10213225/ https://www.ncbi.nlm.nih.gov/pubmed/37252667 http://dx.doi.org/10.3389/fgene.2023.1193953 |
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author | Yu, Liyang Fei, Cao Wang, Dongsheng Huang, Ruimin Xuan, Wang Guo, Chunlei Jing, Liu Meng, Wang Yi, Lu Zhang, Haie Zhang, Jingzheng |
author_facet | Yu, Liyang Fei, Cao Wang, Dongsheng Huang, Ruimin Xuan, Wang Guo, Chunlei Jing, Liu Meng, Wang Yi, Lu Zhang, Haie Zhang, Jingzheng |
author_sort | Yu, Liyang |
collection | PubMed |
description | The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in chestnut (Castanea mollissima), an important nut with high ecological and economic value. In the present study, 94 CmbHLHs were identified in chestnut genome, of which 88 were unevenly distributed on chromosomes, and other six were located on five unanchored scaffolds. Almost all CmbHLH proteins were predicted in the nucleus, and subcellular localization demonstrated the correctness of the above predictions. Based on the phylogenetic analysis, all of the CmbHLH genes were divided into 19 subgroups with distinct features. Abundant cis-acting regulatory elements related to endosperm expression, meristem expression, and responses to gibberellin (GA) and auxin were identified in the upstream sequences of CmbHLH genes. This indicates that these genes may have potential functions in the morphogenesis of chestnut. Comparative genome analysis showed that dispersed duplication was the main driving force for the expansion of the CmbHLH gene family inferred to have evolved through purifying selection. Transcriptome analysis and qRT-PCR experiments showed that the expression patterns of CmbHLHs were different in different chestnut tissues, and revealed some members may have potential functions in chestnut buds, nuts, fertile/abortive ovules development. The results from this study will be helpful to understand the characteristics and potential functions of the bHLH gene family in chestnut. |
format | Online Article Text |
id | pubmed-10213225 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-102132252023-05-27 Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima Yu, Liyang Fei, Cao Wang, Dongsheng Huang, Ruimin Xuan, Wang Guo, Chunlei Jing, Liu Meng, Wang Yi, Lu Zhang, Haie Zhang, Jingzheng Front Genet Genetics The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in chestnut (Castanea mollissima), an important nut with high ecological and economic value. In the present study, 94 CmbHLHs were identified in chestnut genome, of which 88 were unevenly distributed on chromosomes, and other six were located on five unanchored scaffolds. Almost all CmbHLH proteins were predicted in the nucleus, and subcellular localization demonstrated the correctness of the above predictions. Based on the phylogenetic analysis, all of the CmbHLH genes were divided into 19 subgroups with distinct features. Abundant cis-acting regulatory elements related to endosperm expression, meristem expression, and responses to gibberellin (GA) and auxin were identified in the upstream sequences of CmbHLH genes. This indicates that these genes may have potential functions in the morphogenesis of chestnut. Comparative genome analysis showed that dispersed duplication was the main driving force for the expansion of the CmbHLH gene family inferred to have evolved through purifying selection. Transcriptome analysis and qRT-PCR experiments showed that the expression patterns of CmbHLHs were different in different chestnut tissues, and revealed some members may have potential functions in chestnut buds, nuts, fertile/abortive ovules development. The results from this study will be helpful to understand the characteristics and potential functions of the bHLH gene family in chestnut. Frontiers Media S.A. 2023-05-12 /pmc/articles/PMC10213225/ /pubmed/37252667 http://dx.doi.org/10.3389/fgene.2023.1193953 Text en Copyright © 2023 Yu, Fei, Wang, Huang, Xuan, Guo, Jing, Meng, Yi, Zhang and Zhang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Yu, Liyang Fei, Cao Wang, Dongsheng Huang, Ruimin Xuan, Wang Guo, Chunlei Jing, Liu Meng, Wang Yi, Lu Zhang, Haie Zhang, Jingzheng Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima |
title | Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
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title_full | Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
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title_fullStr | Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
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title_full_unstemmed | Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
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title_short | Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima
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title_sort | genome-wide identification, evolution and expression profiles analysis of bhlh gene family in castanea mollissima |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10213225/ https://www.ncbi.nlm.nih.gov/pubmed/37252667 http://dx.doi.org/10.3389/fgene.2023.1193953 |
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