Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus
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RESEARCH ARTICLE
Open Access
Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus Weizhuo Zhu, Yiyi Guo, Yeke Chen, Dezhi Wu*
and Lixi Jiang
Abstract Background: Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion: The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed. Keywords: Brassica napus, GATA, Genome-wide, Expression patterns, SNP distribution
Background Transcription factors (TFs) regulate gene expression by recognizing and combining cis-acting elements on the promoter regions of target genes [1]. TFs play key roles in plant developmental processes, hormones signaling pathways and disease resistance responses. There are several well-known transcription factor families including WRKY, MYB (V-myb avian myeloblastosis viral oncogene homolog), DREB (Dehydration-responsive element-binding protein), bZIP (Basic region-leucine zipper), MADS-box and GATA (GATA-binding factor) in * Correspondence: [email protected] Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
plants. Among them, the GATA genes are characterized as important regulators for many biological processes, such as flower development, carbon and nitrogen metabolisms [2]. The GATA genes could recognize and bind to the (T/A)GATA(A/G) sequences to regulate the transcription levels of their downstream genes [3, 4]. The DNA binding domains of the GATA proteins contain a type IV zinc finger structure C-X2-C-X17–20-C-X2-C and a conserved basic follow region, and most of them featured with C-X2-C-X18-C-X2-C or C-X2-C-X20-C-X2-C zinc finger domains [2, 3, 5, 6]. Generally, the GATA family ge
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