Genome-wide Identification And Analysis Of ALDH And MATE Gene Families In Gossypium

Cotton is an important fiber crop, oil crop and strategic material, which contributes greatly to the agriculture of China. Due to the influence of various factors, cotton growing areas in our country present "to west, to east, to north", the trend of the development of cotton in China will form new cotton belt: the north including saline-alkali land, dryland in northwest of China, drought area of Xinjiang and coastal saline-alkali wetland. The hostile cotton-growing conditions, soil salinity and drought seriously affects the production. Exploring the mechanism of drought resistance and salt tolerance of cotton, and stress resistance breeding, are the urgent direction of current cotton research in china. Aldehyde dehydrogenases(ALDHs) could reduce toxic action of reactive oxygen species(ROS) by eliminating excess aldehydes, to improve plant adaptation to environmental stress. Multidrug and toxic compound extrusion(MATE) proteins are the last family of transporters, which works as secondary carriers. Previous studies have shown that MATE genes involve in the growth and development, resistance to disease and stress in plant. Currently, there are few reasearches on ALDH gene in Gossypium arboreum. In present study, all ALDH genes in Gossypium arboreum genome, MATE genes in Gossypium arboreum and Gossypium raimondii were identified by Bioinformatics approaches. Analysis of the structure of the genes, protein structure domain, synteny and phylogenetic were used to study the evolution of these two familes. Expression profiles of ALDH genes in G. arboreum under various abiotic stresses were analyzed with quantitative real-time RT-PCR. While cis acting elements of MATE genes in Gossypium arboreum and Gossypium raimondii were analyzed. The main results were as fallows:1. We identified 30 ALDH genes in the G. arboreum genome and grouped them into ten families according to amino acid sequence identity. Members of the same family have similarity exon-intron structures and structural domain, and all members of ALDH18 family possess distinct AA-kinase domain. Synteny analysis shows that tandem and segmental duplications played a crucial role in evolution and expansion of ALDH genes in G. arboreum. Phylogenetic and synteny analysis between G. arboreum and G. raimondii demonstrated that all Ga ALDH genes and ALDH genes in G. raimondii are orthologous genes and that most of Ga ALDH genes located in the corresponding syntenic blocks of G. raimondii, implying these genes appeared before the divergence of G. arboreum and G. raimondii and no expansion of ALDH superfamily happened in these two cotton species. Real-time quantitative PCR data revealed that Ga ALDH2B1, Ga ALDH2C4, Ga ALDH18B1, Ga ALDH18B3 were upregulated under salt stress, Ga ALDH2B1, Ga ALDH2C3, Ga ALDH18B1, Ga ALDH18B3 were response to drought.2. Genome-wide identification and anlysis of MATE genes in G. raimondii. 70 Gr MATE genes were identified in the G. raimondii, which are randomly distributed on 13 chromosomes. Most Gr MATE genes are located in segmental duplicated genome regions. There are some cis acting elements in the upstream region of MATE genes in Gossypium raimondii, such as HSE, LTR,MBS, O2-site, ABRE, TCA, which imply that some Gr MATE genes may respond to heat, cold, drought, zinc and SA.3. We identified 68 Ga MATE genes in G. arboreum, with 66 mapped on 13 chromosomes while two(Ga MATE67, Ga MATE68) located on the scaffolds. Compared with G. arboreum, G. raimondii included two more MATE genes. According to phylogenetic analysis, MATE genes were divided into three groups(MATEⅠ, MATEⅡ and MATEⅢ). There is no obvious difference on the number of group MATEⅠ genes between the two cotton species and Arabidopsis thaliana, but gene duplication existing in the MATEⅡ, MATEⅢ group in G. arboreum and G. raimondii, which implies these two group MATE genes playing a role in adaptation to environment. Members of the same group have similar exon-intron structures. Analysis of protein structure domain showed some members of MATEⅢ group contained distinct Polysacc_synt_C domin. Phylogenetic analysis showed that there are 64 orthologous gene pairs between G. raimondii and G. arboreum. Like in G. raimondii, some cis acting elements, such as HSE, LTR, MBS, O2-site, ABRE, TCA, occured in the upstream region of MATE genes in G. arboreum.