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

Li et al. BMC Genomics (2016) 17:1000 DOI 10.1186/s12864-016-3365-z RESEARCH ARTICLE Open Access Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development Weijie Li1,2†, Haihong Shang1†, Qun Ge1, Changsong Zou1, Juan Cai1, Daojie Wang2, Senmiao Fan1, Zhen Zhang1, Xiaoying Deng1, Yunna Tan1, Weiwu Song1, Pengtao Li1, Palanga Kibalou Koffi1, Muhammad Jamshed1, Quanwei Lu1, Wankui Gong1, Junwen Li1, Yuzhen Shi1, Tingting Chen1, Juwu Gong1, Aiying Liu1 and Youlu Yuan1* Abstract Background: 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. Results: 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. Conclusion: 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. Keywords: Cotton, Pectin methylesterases (PMEs), Gene family, Gene structure, Phylogeny, Expression patterns * Correspondence: † Equal contributors 1 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 Full list of author information is available at the end of the article © The Author(s). 2016 Open Access This 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. Li et al. BMC Genomics (2016) 17:1000 Background Cotton (Gossypium spp.) is one of the most important natural fiber crops around the world. The improvement of cotton fiber quality is becoming increasingly important and is now a main focal point of cotton research [1, 2]. Pectin is an important component of cotton fiber and pectin metabolism may influence fiber quality. Previous studies showed that PMEs play an important role in the process of fiber development by influencing the chemical properties of pectin [1]. Process of cotton fiber cell developing was purposely divided into four relative independent but overlapping stages: fiber initiation, elongation, secondary wall biosynthesis and maturation [3]. Fiber initiation and elongation are critical periods in which the number and lengths of fibers, secondary wall thickening (fiber strength), and other fiber quality traits are determined..The secondary wall thickening in cotton fibers starts 15–19 d after flowering and continues to thicken until 40–50d [4]. The increasing thickness of the fiber secondary wall gradually increases the strength of fibers. A forward subtractive cDNA library constructed and sequenced from upland cotton (G. hirsutum) fibers during the secondary cell wall thickening stage. Computational analysis showed differentially expressed genes that may be involved in cell wall synthesis and modification of biological processes. Among them, several differentially expressed genes which encoded PMEs were identified. Thus, in order to elucidate the relationship between PMEs and fiber development, we analyzed identification, phylogeny expression of PMEs in G. arboreum, G. raimondii and G. hirsutum. PMEs are widely present in plants and some microorganisms that possess a cell wall degradation function. PMEs catalyze the demethylesterification of pectin, which generates carboxyl groups during the release of methanol and hydrogen ions [5]. It plays an important role in cell wall composition modification and degradation if pectin in different development stages of plant, such as fruit maturity [6], pollen development and pollen tube growth [7], cambium cell differentiation, and other plant growth and so on. PMEs have a two-part influence on the cell wall. These produce carboxyl groups and combine with extracellular Ca2+ to form a calcium chain bridge between adjacent pectins, thereby hardening the cell wall and slowing cell diffuse growth [8]. And, the reaction of demethylesterification decreases the extracellular pH to increase the hydrolytic enzyme activities of enzymes such as poly-galacturonic acid and several pectin enzyme cleavage enzymes [9]. Pectin is subject to substantial degradation, causes cell wall structure relaxation, and enhances the growth of cell tips [10]. The activity of PMEs is regulated by pectin methylesterase inhibitors (PMEIs) [11] whose active site is the conserved PME domain. All members of PME family Page 2 of 13 consist of a catalytically active zone PME domain; some also harbor a PMEI domain. Some proteins containing only one PMEI domain belong to the PMEI family. Therefore, the predicted proteins can be classified into two categories, type I, containing both PME and PMEI domains, and type II, consisting only a PME domain. The PME belongs to a multigene family which was fir (...truncated)