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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3365-z) contains supplementary material, which is available to authorized users.

Genome wide identification and functional characterization of strawberry pectin methylesterases related to fruit softening

“…As one of the pectin-modifying enzymes, the functionality of PME genes has been widely studied in many plant species, such as Arabidopsis [27], rice [28], flax [30], and cotton [31]. Here, 54 PME genes were identified in strawberry, and 53, 57, 66, 78 and 79 PME genes were found from rose, Chinese plum, peach, apple and pear, respectively (Additional file 2: Table S2).…”

“…[29], flax [30], and Asiatic cotton (Gossypium arboretum) [31]. All PME genes from those species contain a catalytically active zone PME domain, and some of them also comprise a pectin methylesterase inhibitor (PMEI) domain [27,28,30,31]. With expression assay, those studies found some candidate PME genes which have tissue-specific expression patterns.…”

“…With expression assay, those studies found some candidate PME genes which have tissue-specific expression patterns. For example, eight PMEs from cotton showed fiber predominant expression in secondary wall thickening, which provided an important basis for further research on the functions of PMEs in cotton fiber development [31]. Although PME has been well characterized in model plants, knowledge regarding the functionality and evolutionary property of PME gene family in Rosaceae plant species remain limited.…”

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

“…1 , Additional file 2 : Table S2). The PELs of Oryza sativa were located a long distance from those of the other plants, which might be related to different functions of these proteins between monocots and dicots [ 39 ]. All of the GhPELs exhibited the conserved Pec_lyase_C domain, with highly conserve Ca 2+ -binding, disulfide bonds, catalysis and substrate binding amino acid sites (Additional file 6 : Figure S1 and Additional file 7 : Fig.…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…The differences in the PMEs expression levels at the developmental stage of fiber was observed using qRT-PCR. Predominant expression in fiber was during the secondary cell wall thickening stage suggesting tissue-specific expression patterns in cotton fiber [94].…”