Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>

As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an i...

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Autores principales:	Yang Ye, Haodong Xin, Xiting Gu, Jianwen Ma, Lingli Li
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Populus trichocarpa</i> genome-wide analysis <i>PtHLHs</i> <i>PtFBHs</i> expression analysis flowering process Plant ecology QK900-989
Acceso en línea:	https://doaj.org/article/e5248aec7ac84475ba6fc5426ce68181
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spelling	oai:doaj.org-article:e5248aec7ac84475ba6fc5426ce681812021-11-25T17:37:17ZGenome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>10.3390/f121114391999-4907https://doaj.org/article/e5248aec7ac84475ba6fc5426ce681812021-10-01T00:00:00Zhttps://www.mdpi.com/1999-4907/12/11/1439https://doaj.org/toc/1999-4907As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the <i>bHLHs</i> and <i>FBHs</i> gene family in the newest version of <i>Populus</i><i>trichocarpa</i> genome have not been analyzed yet. We identified 233 <i>PtbHLHs</i> and 10 <i>PtFBHs</i> in the newest version genome, and <i>PtbHLHs</i> were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These <i>PtHLHs</i> were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the <i>PtbHLHs</i> gene family has undergone strong purification selection during the evolution process. The <i>cis</i>-elements analysis has suggested that <i>PtbHLHs</i> may be related to the growth and development. Conserved residues of FBHs among <i>Arabidopsis</i> and poplar were also identified. Expression of 227 <i>PtHLH</i> genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of <i>PtbHLH</i> and <i>PtFBH</i> family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of <i>PtbHLHs</i>.Yang YeHaodong XinXiting GuJianwen MaLingli LiMDPI AGarticle<i>Populus trichocarpa</i>genome-wide analysis<i>PtHLHs</i><i>PtFBHs</i>expression analysisflowering processPlant ecologyQK900-989ENForests, Vol 12, Iss 1439, p 1439 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Populus trichocarpa</i> genome-wide analysis <i>PtHLHs</i> <i>PtFBHs</i> expression analysis flowering process Plant ecology QK900-989
spellingShingle	<i>Populus trichocarpa</i> genome-wide analysis <i>PtHLHs</i> <i>PtFBHs</i> expression analysis flowering process Plant ecology QK900-989 Yang Ye Haodong Xin Xiting Gu Jianwen Ma Lingli Li Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
description	As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the <i>bHLHs</i> and <i>FBHs</i> gene family in the newest version of <i>Populus</i><i>trichocarpa</i> genome have not been analyzed yet. We identified 233 <i>PtbHLHs</i> and 10 <i>PtFBHs</i> in the newest version genome, and <i>PtbHLHs</i> were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These <i>PtHLHs</i> were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the <i>PtbHLHs</i> gene family has undergone strong purification selection during the evolution process. The <i>cis</i>-elements analysis has suggested that <i>PtbHLHs</i> may be related to the growth and development. Conserved residues of FBHs among <i>Arabidopsis</i> and poplar were also identified. Expression of 227 <i>PtHLH</i> genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of <i>PtbHLH</i> and <i>PtFBH</i> family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of <i>PtbHLHs</i>.
format	article
author	Yang Ye Haodong Xin Xiting Gu Jianwen Ma Lingli Li
author_facet	Yang Ye Haodong Xin Xiting Gu Jianwen Ma Lingli Li
author_sort	Yang Ye
title	Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
title_short	Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
title_full	Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
title_fullStr	Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
title_full_unstemmed	Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>
title_sort	genome-wide identification and functional analysis of the basic helix-loop-helix (bhlh) transcription family reveals candidate <i>ptfbh</i> genes involved in the flowering process of <i>populus trichocarpa</i>
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/e5248aec7ac84475ba6fc5426ce68181
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Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate <i>PtFBH</i> Genes Involved in the Flowering Process of <i>Populus trichocarpa</i>

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