Genome-Wide Analysis of Multidrug and Toxic Compound Extrusion (MATE) Family in Gossypium raimondii and Gossypium arboreum and Its Expression Analysis Under Salt, Cadmium, and Drought Stress

Abstract

The extrusion of toxins and substances at a cellular level is a vital life process in plants under abiotic stress. The multidrug and toxic compound extrusion (MATE) gene family plays a large role in the exportation of toxins and other substrates. We carried out a genome-wide analysis of MATE gene families in Gossypium raimondii and Gossypium arboreum and assessed their expression levels under salt, cadmium and drought stresses. We identified 70 and 68 MATE genes in G. raimondii and G. arboreum, respectively. The majority of the genes were predicted to be localized within the plasma membrane, with some distributed in other cell parts. Based on phylogenetic analysis, the genes were subdivided into three subfamilies, designated as M1, M2 and M3. Closely related members shared similar gene structures, and thus were highly conserved in nature and have mainly evolved through purifying selection. The genes were distributed in all chromosomes. Twenty-nine gene duplication events were detected, with segmental being the dominant type. GO annotation revealed a link to salt, drought and cadmium stresses. The genes exhibited differential expression, with GrMATE18, GrMATE34, GaMATE41 and GaMATE51 significantly upregulated under drought, salt and cadmium stress, and these could possibly be the candidate genes. Our results provide the first data on the genome-wide and functional characterization of MATE genes in diploid cotton, and are important for breeders of more stress-tolerant cotton genotypes.

Keywords: GO annotation; GenPred; Genomic Selection; Gossypium arboreum; Gossypium raimondii; MATE genes; Shared Data Resources; cadmium; drought; phylogenetic tree analysis; stress.

Figure 1

Phylogenetic relationship of MATE genes in two diploid cotton species with Arabidopsis. Neighbor-joining phylogeny of 68 genes for G. arboreum, 70 genes for G. raimondii, and 58 Arabidopsis MATE protein sequences, as constructed by MEGA 6.0. The different colors mark the various MATE gene types.

Figure 2

Phylogenetic tree and gene structure of MATE genes in diploid cotton. The phylogenetic tree was constructed using MEGA 6.0. Exon/intron structures of MATE genes are shown. A. Phylogenetic tree and structure for MATE genes of G. arboreum. B. Phylogenetic tree and structure for MATE genes of G. raimondii.

Figure 3

MATE gene distribution in genome A and genome D cotton chromosomes. A: chromosome mapping of GaMATE genes; B: chromosome mapping of GrMATE genes. Chromosomal position of each MATE gene was mapped according to the diploid cotton genome. The chromosome number is indicated at the top of each chromosome. Red indicates genes that showed a high level of collinearity. Duplicated genes are shown in black boxes.

Figure 4

Syntenic relationships among MATE genes from G. raimondii and G. arboreum. G. raimondii and G. arboreum chromosomes are indicated in different colors. The putative orthologous MATE genes between G. raimondii and G. arboreum are represented in red. The chromosome number and the gene names are indicated around the outside of the figure.

Figure 5

Average number of cis-promoter elements in the regions of G. raimondii and G. arboreum MATE genes. The cis-promoters were analyzed in the 1 kb up/down stream promoter regions of translation start site, using the PLACE database.

Figure 6

Gene ontology (GO) annotation results for diploid cotton MATE genes. GO analysis of (A) upregulated and (B) downregulated MATE protein sequences predicted for their involvement in biological processes, molecular functions, and cellular processes.

Figure 7

Pore morphology, dimensions, and protein topology of G. arboreum and G. raimondii MATE proteins. (A and D) Protein tertiary structures showing pore morphology of MATE family members. (B and E) Graphs showing pore dimensions obtained from PoreWalker software. (C and F) Topology of two examples of two MATE proteins.

Figure 8

Differential expression of diploid cotton MATE genes under drought, salt, and Cd stress. The heat map was visualized using the MeV_4_9_0 program. Red and green indicate high and low levels of expression, respectively. (A) Heat map showing 24 GaMATE genes. (B) Heat map for the 63 genes of G. raimondii (GrMATEs).