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Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)

BACKGROUND: Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, th...

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Autores principales: Sun, Huiru, Hao, Pengbo, Ma, Qiang, Zhang, Meng, Qin, Yuan, Wei, Hengling, Su, Junji, Wang, Hantao, Gu, Lijiao, Wang, Nuohan, Liu, Guoyuan, Yu, Shuxun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131898/
https://www.ncbi.nlm.nih.gov/pubmed/30200887
http://dx.doi.org/10.1186/s12864-018-5047-5
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author Sun, Huiru
Hao, Pengbo
Ma, Qiang
Zhang, Meng
Qin, Yuan
Wei, Hengling
Su, Junji
Wang, Hantao
Gu, Lijiao
Wang, Nuohan
Liu, Guoyuan
Yu, Shuxun
author_facet Sun, Huiru
Hao, Pengbo
Ma, Qiang
Zhang, Meng
Qin, Yuan
Wei, Hengling
Su, Junji
Wang, Hantao
Gu, Lijiao
Wang, Nuohan
Liu, Guoyuan
Yu, Shuxun
author_sort Sun, Huiru
collection PubMed
description BACKGROUND: Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton. RESULTS: We identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively. These PEL genes were classified into five subfamilies (I-V). Members from the same subfamilies showed relatively conserved gene structures, motifs and protein domains. An analysis of gene chromosomal locations and gene duplication revealed that segmental duplication likely contributed to the expansion of the GhPELs. The 2000 bp upstream sequences of all the GhPELs contained auxin response elements. A transcriptomic data analysis showed that 62 GhPELs were expressed in various tissues. Notably, most (29/32) GhPELs of subfamily IV were preferentially expressed in the stamen, and five GhPELs of subfamily V were prominently expressed at the fiber elongation stage. In addition, qRT-PCR analysis revealed the expression characteristics of 24 GhPELs in four pollen developmental stages and significantly different expression of some GhPELs between long- and short-fiber cultivars. Moreover, some members were responsive to IAA treatment. The results indicate that GhPELs play significant and functionally diverse roles in the development of different tissues. CONCLUSIONS: In this study, we comprehensively analyzed PELs in G. hirsutum, providing a foundation to better understand the functions of GhPELs in different tissues and pathways, especially in pollen, fiber and the auxin signaling pathway. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5047-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-61318982018-09-13 Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.) Sun, Huiru Hao, Pengbo Ma, Qiang Zhang, Meng Qin, Yuan Wei, Hengling Su, Junji Wang, Hantao Gu, Lijiao Wang, Nuohan Liu, Guoyuan Yu, Shuxun BMC Genomics Research Article BACKGROUND: Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton. RESULTS: We identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively. These PEL genes were classified into five subfamilies (I-V). Members from the same subfamilies showed relatively conserved gene structures, motifs and protein domains. An analysis of gene chromosomal locations and gene duplication revealed that segmental duplication likely contributed to the expansion of the GhPELs. The 2000 bp upstream sequences of all the GhPELs contained auxin response elements. A transcriptomic data analysis showed that 62 GhPELs were expressed in various tissues. Notably, most (29/32) GhPELs of subfamily IV were preferentially expressed in the stamen, and five GhPELs of subfamily V were prominently expressed at the fiber elongation stage. In addition, qRT-PCR analysis revealed the expression characteristics of 24 GhPELs in four pollen developmental stages and significantly different expression of some GhPELs between long- and short-fiber cultivars. Moreover, some members were responsive to IAA treatment. The results indicate that GhPELs play significant and functionally diverse roles in the development of different tissues. CONCLUSIONS: In this study, we comprehensively analyzed PELs in G. hirsutum, providing a foundation to better understand the functions of GhPELs in different tissues and pathways, especially in pollen, fiber and the auxin signaling pathway. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5047-5) contains supplementary material, which is available to authorized users. BioMed Central 2018-09-10 /pmc/articles/PMC6131898/ /pubmed/30200887 http://dx.doi.org/10.1186/s12864-018-5047-5 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Sun, Huiru
Hao, Pengbo
Ma, Qiang
Zhang, Meng
Qin, Yuan
Wei, Hengling
Su, Junji
Wang, Hantao
Gu, Lijiao
Wang, Nuohan
Liu, Guoyuan
Yu, Shuxun
Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title_full Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title_fullStr Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title_full_unstemmed Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title_short Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
title_sort genome-wide identification and expression analyses of the pectate lyase (pel) gene family in cotton (gossypium hirsutum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131898/
https://www.ncbi.nlm.nih.gov/pubmed/30200887
http://dx.doi.org/10.1186/s12864-018-5047-5
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