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

Abstract

The GATA proteins, functioning as transcription factors (TFs), are involved in multiple plant physiological and biochemical processes. In this study, 28 GATA TFs of Brachypodium distachyon (BdGATA) were systematically characterized via whole-genome analysis. BdGATA genes unevenly distribute on five chromosomes of B. distachyon and undergo purifying selection during the evolution process. The putative cis-acting regulatory elements and gene interaction network of BdGATA were found to be associated with hormones and defense responses. Noticeably, the expression profiles measured by quantitative real-time PCR indicated that BdGATA genes were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatment, and 10 of them responded to invasion of the fungal pathogen Magnaporthe oryzae, which causes rice blast disease. Genome-wide characterization, evolution, and expression profile analysis of BdGATA genes can open new avenues for uncovering the functions of the GATA genes family in plants and further improve the knowledge of cellular signaling in plant defense.

Keywords: Brachypodium distachyon; GATA transcription factors; genome-wide characterization; phylogenetic analysis; profile analysis.

Figure 1

Phylogenetic tree of GATA proteins from Brachypodium distachyon, rice, and wheat. Phylogenetic relationships of GATA proteins from Brachypodium distachyon (28), rice (26), and wheat (29) were performed with MEGA v5.0 using the NJ method with 1000 bootstrap replicates. The GATA proteins were clustered into four major groups—A, B, C, and D. Members of B. distachyon, rice, and wheat are represented by purple circles, blue stars, and red triangles, respectively. Gene IDs of GATAs from B. distachyon, rice and wheat were listed in Table S2.

Figure 2

Chromosomal locations of BdGATA with gene density. The size of a chromosome is estimated from its relative length. The chromosome numbers are shown on the left of each chromosome. The gene density is indicated by the color bar (blue-to-red scale indicates gene density from low to high).

Figure 3

Duplication pairs and synteny analysis of GATA genes between Brachypodium distachyon and rice/wheat. (A) Each chromosome is represented with a different color. Gray curves denote the details of syntenic regions in Brachypodium distachyon genome and red curves denote BdGATA gene pairs with segmental duplication. (B) Red lines indicate homologous genes between Brachypodium distachyon and rice/wheat chromosomes.

Figure 4

Putative conserved motifs, domains, and gene structures of the BdGATA family. (A) Phylogenetic tree. Multiple sequence alignment of BdGATA proteins was performed using ClustalX. The neighbor-joining tree was constructed using MEGA v5.0 with 1000 bootstrap replicates. (B) Conserved motifs. MEME Suite version 5.1.1 revealed the conserved motifs of the GATA proteins. (C) The distribution of conserved domains of BdGATA family. aa: amino acids. (D) Gene structure. The blue square, green square, and black lines represent the exon, untranslated region (UTR), and intron, respectively.

Figure 5

Interaction network of GATA and related genes. Line thickness indicates the strength of data support. The associations were inferred from the evidence from the STRING database—known interactions, predicted interactions, and others.

Figure 6

RT-PCR analysis of BdGATA expression in different tissues of Brachypodium distachyon.

Figure 7

Expression profiles of BdGATA genes with phytohormone treatments. (A) Fold change in expression of BdGATA genes after hormone treatments. Fold change in BdGATA gene expression after hormone treatments assessed by qRT-PCR of cDNA isolated from hormone treatment plants were compared with mock treatment plants. Fold change of 1 means no difference in gene expression between hormone treatment plants and mock treatment plants. This assay was repeated three times with similar results. (B) Box–whisker plot of BdGATA gene expression after phytohormone treatments. The y-axis represents relative gene expression level. Whiskers represent maximum/minimum values, boxes indicate the first quartile and third quartile, and the horizontal line represents the median.

Figure 8

Expression of BdGATA genes inoculated with Magnaporthe oryzae. The relative expression levels of BdGATA genes were normalized with BdUBC. The experiments in all panels were repeated three times with similar results.