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Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus

Zhang, Zhen, Zou, Xianyan, Huang, Zhen, Fan, Senmiao, Qun, Ge, Liu, Aiying, Gong, Juwu, Li, Junwen, Gong, Wankui, Shi, Yuzhen, Fan, Liqiang, Zhang, Zhibin, Liu, Ruixian, Jiang, Xiao, Lei, Kang, Shang, Haihong, Xu, Aixia, Yuan, Youlu
Gene 2019 v.680 pp. 72-83
Arabidopsis thaliana, DNA, GATA transcription factors, Glycine max, Gossypium arboreum, Gossypium hirsutum, Gossypium raimondii, Oryza sativa, cell differentiation, cotton, fiber quality, gene expression, genes, phylogeny, plant tissues, quantitative polymerase chain reaction, quantitative trait loci, reverse transcriptase polymerase chain reaction, sequence analysis, zinc finger motif
GATA transcription factors (TFs), which bind to DNA in regulatory regions, are involved in cell differentiation and possess a type-IV zinc finger and a DNA-binding domain. GATA genes have been characterized in plant species such as Arabidopsis thaliana, Oryza sativa, and Glycine max, and their functions have been elucidated in A. thaliana. Although many Gossypium quantitative trait loci for fiber quality harbor GATA TFs, GATA genes have not yet been characterized in cotton. In this study, we identified 179 GATA genes from the genomes of three Gossypium species. We analyzed the phylogenetic relationships, chromosomal distribution, gene structure, expression pattern, and predicted promoters of all 179 Gossypium GATA genes (46 in G. raimondii, 46 in G. arboreum, and 87 in G. hirsutum). Phylogenetic analysis grouped the 179 GATA genes into four subfamilies. Domain analysis revealed that GATA domains in subfamilies I, II, and III were located near the C-terminal, whereas those in subfamily IV were adjacent to the N-terminal. RNA-seq and (Real-time PCR) qRT-PCR revealed that 39.1% (34/87) of GATA genes were expressed in growing plant tissues in G. hirsutum, but only 12.6% (11/87) were expressed during fiber development. In addition, 45.7% (21/46) and 26.1% (12/46) of GATA genes were expressed in G. arboreum and G. raimondii, respectively. Our results may be useful for elucidating the evolution, expression patterns, and functional divergence of GATA genes in Gossypium.