Cargando…

Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea

Plant polygalacturonases (PGs) are closely related to cell-separation events during plant growth and development by degrading pectin. Identifying and investigating their diversification of evolution and expression could shed light on research on their function. We conducted sequence, molecular evolu...

Descripción completa

Detalles Bibliográficos
Autores principales: Lyu, Meiling, Iftikhar, Junaid, Guo, Rongfang, Wu, Binghua, Cao, Jiashu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461206/
https://www.ncbi.nlm.nih.gov/pubmed/32784897
http://dx.doi.org/10.3390/ijms21165706
_version_ 1783576728519573504
author Lyu, Meiling
Iftikhar, Junaid
Guo, Rongfang
Wu, Binghua
Cao, Jiashu
author_facet Lyu, Meiling
Iftikhar, Junaid
Guo, Rongfang
Wu, Binghua
Cao, Jiashu
author_sort Lyu, Meiling
collection PubMed
description Plant polygalacturonases (PGs) are closely related to cell-separation events during plant growth and development by degrading pectin. Identifying and investigating their diversification of evolution and expression could shed light on research on their function. We conducted sequence, molecular evolution, and gene expression analyses of PG genes in Brassica oleracea. Ninety-nine B. oleracea PGs (BoPGs) were identified and divided into seven clades through phylogenetic analysis. The exon/intron structures and motifs were conserved within, but divergent between, clades. The second conserved domain (GDDC) may be more closely related to the identification of PGs. There were at least 79 common ancestor PGs between Arabidopsis thaliana and B. oleracea. The event of whole genome triplication and tandem duplication played important roles in the rapid expansion of the BoPG gene family, and gene loss may be an important mechanism in the generation of the diversity of BoPGs. By evaluating the expression in five tissues, we found that most of the expressed BoPGs in clades A, B, and E showed ubiquitous expression characteristics, and the expressed BoPGs in clades C, D, and F were mainly responsible for reproduction development. Most of the paralogous gene pairs (76.2%) exhibited divergent expression patterns, indicating that they may have experienced neofunctionalization or subfunctionalization. The cis-elements analysis showed that up to 96 BoPGs contained the hormone response elements in their promoters. In conclusion, our comparative analysis may provide a valuable data foundation for the further functional analysis of BoPGs during the development of B. oleracea.
format Online
Article
Text
id pubmed-7461206
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-74612062020-09-14 Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea Lyu, Meiling Iftikhar, Junaid Guo, Rongfang Wu, Binghua Cao, Jiashu Int J Mol Sci Article Plant polygalacturonases (PGs) are closely related to cell-separation events during plant growth and development by degrading pectin. Identifying and investigating their diversification of evolution and expression could shed light on research on their function. We conducted sequence, molecular evolution, and gene expression analyses of PG genes in Brassica oleracea. Ninety-nine B. oleracea PGs (BoPGs) were identified and divided into seven clades through phylogenetic analysis. The exon/intron structures and motifs were conserved within, but divergent between, clades. The second conserved domain (GDDC) may be more closely related to the identification of PGs. There were at least 79 common ancestor PGs between Arabidopsis thaliana and B. oleracea. The event of whole genome triplication and tandem duplication played important roles in the rapid expansion of the BoPG gene family, and gene loss may be an important mechanism in the generation of the diversity of BoPGs. By evaluating the expression in five tissues, we found that most of the expressed BoPGs in clades A, B, and E showed ubiquitous expression characteristics, and the expressed BoPGs in clades C, D, and F were mainly responsible for reproduction development. Most of the paralogous gene pairs (76.2%) exhibited divergent expression patterns, indicating that they may have experienced neofunctionalization or subfunctionalization. The cis-elements analysis showed that up to 96 BoPGs contained the hormone response elements in their promoters. In conclusion, our comparative analysis may provide a valuable data foundation for the further functional analysis of BoPGs during the development of B. oleracea. MDPI 2020-08-09 /pmc/articles/PMC7461206/ /pubmed/32784897 http://dx.doi.org/10.3390/ijms21165706 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lyu, Meiling
Iftikhar, Junaid
Guo, Rongfang
Wu, Binghua
Cao, Jiashu
Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title_full Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title_fullStr Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title_full_unstemmed Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title_short Patterns of Expansion and Expression Divergence of the Polygalacturonase Gene Family in Brassica oleracea
title_sort patterns of expansion and expression divergence of the polygalacturonase gene family in brassica oleracea
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461206/
https://www.ncbi.nlm.nih.gov/pubmed/32784897
http://dx.doi.org/10.3390/ijms21165706
work_keys_str_mv AT lyumeiling patternsofexpansionandexpressiondivergenceofthepolygalacturonasegenefamilyinbrassicaoleracea
AT iftikharjunaid patternsofexpansionandexpressiondivergenceofthepolygalacturonasegenefamilyinbrassicaoleracea
AT guorongfang patternsofexpansionandexpressiondivergenceofthepolygalacturonasegenefamilyinbrassicaoleracea
AT wubinghua patternsofexpansionandexpressiondivergenceofthepolygalacturonasegenefamilyinbrassicaoleracea
AT caojiashu patternsofexpansionandexpressiondivergenceofthepolygalacturonasegenefamilyinbrassicaoleracea