title: Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development.
abstract: Pectin 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.
  
  
  
  We 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.
  
  
  
  Conserved 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.
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.|State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China.
authors.forename: Weijie
authors.initials: W
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Changsong
authors.initials: C
authors.lastname: Zou
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China.
authors.forename: Daojie
authors.initials: D
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Senmiao
authors.initials: S
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Yunna
authors.initials: Y
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Weiwu
authors.initials: W
authors.lastname: Song
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Pengtao
authors.initials: P
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Palanga Kibalou
authors.initials: PK
authors.lastname: Koffi
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Jamshed
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Quanwei
authors.initials: Q
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Wankui
authors.initials: W
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Juwu
authors.initials: J
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
authors.forename: Aiying
authors.initials: A
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. youluyuan@hotmail.com.
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
mesh_terms: D002265:Carboxylic Ester Hydrolases / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D032561:Cotton Fiber; D004789:Enzyme Activation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D003368:Gossypium / Q000145:classification* / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D015203:Reproducibility of Results; D059467:Transcriptome
chemical_list: D002265:Carboxylic Ester Hydrolases; C022323:pectinesterase
keywords: Cotton; Expression patterns; Gene family; Gene structure; Pectin methylesterases (PMEs); Phylogeny