Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development

BMC Genomics

Research Article

Daojie Wang¹  Weiwu Song²  Aiying Liu²  Zhen Zhang²  Youlu Yuan²  Wankui Gong²  Haihong Shang²  Palanga Kibalou Koffi²  Pengtao Li²  Juwu Gong²  Yuzhen Shi²  Senmiao Fan²  Qun Ge²  Xiaoying Deng²  Changsong Zou²  Juan Cai²  Junwen Li²  Tingting Chen²  Yunna Tan²  Quanwei Lu²  Muhammad Jamshed²  Weijie Li³ 

[1] State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, 475004, Kaifeng, China;State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, Henan, China;State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, Henan, China;State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, 475004, Kaifeng, China;

关键词: Cotton;    PMEs;    Gene family;    Gene structure;    Phylogeny;    Expression patterns;   

DOI  :  10.1186/s12864-016-3365-z

 received in 2016-02-27, accepted in 2016-12-02,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundPectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme that utilizes pectin as substrates, and plays a significant role in regulating pectin reconstruction thereby regulating plant growth. Pectin is one of the important components of the plant cell wall, which forms the main structural material of cotton fiber. In this research, cotton genome information was used to identify PMEs.ResultsWe identified 80 (GaPME01-GaPME80) PME genes from diploid G. arboreum (A genome), 78 (GrPME01-GrPME78) PME genes from G. raimondii (D genome), and 135 (GhPME001-GhPME135) PME genes from tetraploid cotton G. hirsutum (AD genome). We further analyzed their gene structure, conserved domain, gene expression, and systematic evolution to lay the foundation for deeper research on the function of PMEs. Phylogenetic data indicated that members from the same species demonstrated relatively high sequence identities and genetic similarities. Analysis of gene structures showed that most of the PMEs genes had 2–3 exons, with a few having a variable number of exons from 4 to 6. There are nearly no differences in the gene structure of PMEs among the three (two diploid and one tetraploid) cotton species. Selective pressure analysis showed that the Ka/Ks value for each of the three cotton species PME families was less than one.ConclusionConserved domain analysis showed that PMEs members had a relatively conserved C-terminal pectinesterase domain (PME) while the N-terminus was less conserved. Moreover, some of the family members contained a pectin methylesterase inhibitor (PMEI) domain. The Ka/Ks ratios suggested that the duplicated PMEs underwent purifying selection after the duplication events. This study provided an important basis for further research on the functions of cotton PMEs. Results from qRT-PCR indicated that the expression level of different PMEs at various fiber developmental stages was different. Moreover, some of the PMEs showed fiber predominant expression in secondary wall thickening indicating tissue-specific expression patterns.

【 授权许可】

CC BY   
© The Author(s). 2016