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Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba

Basic helix–loop–helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In recent years, many bHLH family genes have been identified and characterized in woody plants. However, a...

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Autores principales: Zhou, Xian, Liao, Yongling, Kim, Soo-Un, Chen, Zexiong, Nie, Gongping, Cheng, Shuiyuan, Ye, Jiabao, Xu, Feng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426926/
https://www.ncbi.nlm.nih.gov/pubmed/32792673
http://dx.doi.org/10.1038/s41598-020-69305-3
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author Zhou, Xian
Liao, Yongling
Kim, Soo-Un
Chen, Zexiong
Nie, Gongping
Cheng, Shuiyuan
Ye, Jiabao
Xu, Feng
author_facet Zhou, Xian
Liao, Yongling
Kim, Soo-Un
Chen, Zexiong
Nie, Gongping
Cheng, Shuiyuan
Ye, Jiabao
Xu, Feng
author_sort Zhou, Xian
collection PubMed
description Basic helix–loop–helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In recent years, many bHLH family genes have been identified and characterized in woody plants. However, a systematic analysis of the bHLH gene family has not been reported in Ginkgo biloba, the oldest relic plant species. In this study, we identifed a total of 85 GbbHLH genes from the genomic and transcriptomic databases of G. biloba, which were classified into 17 subfamilies based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon–intron range in GbbHLHs from 0 to 12. The MEME analysis showed that two conserved motifs, motif 1 and motif 2, distributed in most GbbHLH protein. Subcellular localization analysis exhibited that most GbbHLHs located in nucleus and a few GbbHLHs were distributed in chloroplast, plasma membrane and peroxisome. Promoter cis-element analysis revealed that most of the GbbHLH genes contained abundant cis-elements that involved in plant growth and development, secondary metabolism biosynthesis, various abiotic stresses response. In addition, correlation analysis between gene expression and flavonoid content screened seven candidate GbbHLH genes involved in flavonoid biosynthesis, providing the targeted gene encoding transcript factor for increase the flavonoid production through genetic engineering in G. biloba.
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spelling pubmed-74269262020-08-14 Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba Zhou, Xian Liao, Yongling Kim, Soo-Un Chen, Zexiong Nie, Gongping Cheng, Shuiyuan Ye, Jiabao Xu, Feng Sci Rep Article Basic helix–loop–helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In recent years, many bHLH family genes have been identified and characterized in woody plants. However, a systematic analysis of the bHLH gene family has not been reported in Ginkgo biloba, the oldest relic plant species. In this study, we identifed a total of 85 GbbHLH genes from the genomic and transcriptomic databases of G. biloba, which were classified into 17 subfamilies based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon–intron range in GbbHLHs from 0 to 12. The MEME analysis showed that two conserved motifs, motif 1 and motif 2, distributed in most GbbHLH protein. Subcellular localization analysis exhibited that most GbbHLHs located in nucleus and a few GbbHLHs were distributed in chloroplast, plasma membrane and peroxisome. Promoter cis-element analysis revealed that most of the GbbHLH genes contained abundant cis-elements that involved in plant growth and development, secondary metabolism biosynthesis, various abiotic stresses response. In addition, correlation analysis between gene expression and flavonoid content screened seven candidate GbbHLH genes involved in flavonoid biosynthesis, providing the targeted gene encoding transcript factor for increase the flavonoid production through genetic engineering in G. biloba. Nature Publishing Group UK 2020-08-13 /pmc/articles/PMC7426926/ /pubmed/32792673 http://dx.doi.org/10.1038/s41598-020-69305-3 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Zhou, Xian
Liao, Yongling
Kim, Soo-Un
Chen, Zexiong
Nie, Gongping
Cheng, Shuiyuan
Ye, Jiabao
Xu, Feng
Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title_full Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title_fullStr Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title_full_unstemmed Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title_short Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
title_sort genome-wide identification and characterization of bhlh family genes from ginkgo biloba
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426926/
https://www.ncbi.nlm.nih.gov/pubmed/32792673
http://dx.doi.org/10.1038/s41598-020-69305-3
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