Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

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.

Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

“…In terms of multiple sequences alignment, subfamily B of BdGATA genes contain two additional domains, CCT and TIFY, in addition to the fully conserved GATA domain. This is consistent with the conclusion previously reported for dicot plant Brassica napus and monocot plant Zea mays [ 30 , 31 ].…”

Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber (Cucumis sativus L.)

“…The first plant GATA gene (NTL1) was cloned from Nicotiana tabacum [6]. The GATA family was subsequently identified in a number of plants, such as Oryza sativa [3], Arabidopsis thaliana [3,7], Glycine max [8], Malus domestica [9], Vitis vinifera [10], Solanum lycopersicum [11], Gossypium raimondii, Gossypium arboreum, Gossypium hirsutum [12], Brassica napus [13], Brachypodium distachyon [14], Capsicum annuum [15] and so on. In higher plants, GATA genes are involved in various biological processes.…”

“…However, the GATA transcription factors family has not been identified in cucumber. In addition, the functional analysis of GATA transcription factors mainly focused on the abiotic stress such as low nitrogen [8], light [9], cold, drought, salt [11,13] and phytohormones [10,14], but lack of expression patterns analysis of GATA genes in response to biotic stress. Therefore, in this study, we performed the systematic bioinformatics analysis of GATA transcription factors and analyzed the expression profiles of GATA family genes under the abiotic and biotic stresses in cucumber, which provides valuable information and candidate genes for cucumber resistance breeding.…”

Genome-Wide and Comprehensive Analysis of the Multiple Stress-Related CAF1 (CCR4-Associated Factor 1) Family and Its Expression in Poplar

“…In addition, we analyzed the duplication events of PtCAF1 genes in the P. trichocarpa genome ( Figure 5 ), because gene replication plays an important role in the occurrence of novel functions and gene expansion. Analyses of homologous protein families are of great significance in establishing the kinship of species and predicting the function of new protein sequences [ 34 , 35 ]. On the basis of the phylogenetic relationships, the duplication events were proposed to occur in the P. trichocarpa genome.…”