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.

Keywords: Brassica napus; Expression patterns; GATA; Genome-wide; SNP distribution.

Fig. 1

Phylogenetic analysis of GATA proteins in B. napus and A. thaliana. The different-colored arcs indicate subfamilies of the GATA proteins. The unrooted Neighbour-Joining phylogenetic tree was constructed using MEGA7 with full-length amino acid sequences of 126 GATA proteins, and the bootstrap test replicate was set as 1000 times. The asterisks and triangles represent the GATA proteins from B. napus and A. thaliana, respectively

Fig. 2

Schematic representation of phylogenetic relationships, gene structures and conserved motifs of the GATA genes in B. napus. a Phylogenetic tree of 96 BnGATA proteins. The unrooted neighbor-joining phylogenetic tree was constructed with MEGA7 using full-length amino acid sequences of 96 BnGATA proteins, and the bootstrap test replicate was set as 1000 times. b Exon/intron structures of BnGATA genes. Yellow boxes represent exons and black lines represent introns. The UTR region of BnGATA genes are indicated in green boxes. The length of exons can be inferred by the scale at the bottom. c The motif composition of BnGATA proteins. The motifs, numbers 1–10, are displayed in different colored boxes. The sequence information for each motif is provided in Table S4. The length of protein can be estimated using the scale at the bottom

Fig. 3

Alignments of GATA domain sequences of the GATA family members in B. napus. Highly conserved amino acid positions are marked with letters and triangles at the bottom

Fig. 4

The chromosomal distribution and synteny analysis of BnGATA genes in B. napus. The locations of all the BnGATA genes are depicted in the chromosomes. Blue-colored genes belong to subfamily I, green-colored genes belong to subfamily II, orange-colored genes belong to subfamily III, red-colored genes belong to subfamily IV. Background gray lines indicate all B. napus genome synteny blocks, and the red lines highlight the duplicated BnGATA gene pairs. ID of the chromosomes is indicated at the bottom of each chromosome

Fig. 5

Synteny analysis of GATA genes between B .napus and A. thaliana. Gray lines indicate all collinear blocks within B. napus and A. thaliana, while the red lines depict the orthologous relationships of GATA genes between B. napus and A. thaliana

Fig. 6

Expression profiles of BnGATA genes in different tissues. Expression data were processed with log₂ normalization. The color scale represents relative expression levels from high (red colored) to low (blue color)

Fig. 7

Expression profiles of BnGATA genes under abiotic stress condition. Expression profiles were shown as the ratios of the values of the treatments to the controls and processed with log₂ normalization. The color scale represents relative expression levels from high (red colored) to low (blue color)

Fig. 8

Gene structures and SNPs location of BnGATA1.29 and BnGATA2.5. 8 and 10 SNPs were identified in BnGATA1.29 (a) and BnGATA2.5 (b) respectively. SNPs location is indicated with black triangle