Genome-wide identification of GATA family genes in sweet potato (Ipomoea batatas L.) and their expression patterns under abiotic stress

Abstract

GATAs, a type of zinc finger protein transcription factors, can bind to DNA regulatory regions to control the expression of target genes, thereby affecting plant growth and development under normal conditions or environmental stress. However, the GATA gene family has not been identified in sweet potato. In this study, a total of 35, 33, 34, 39, 63, and 56 GATA genes were identified in sweet potato, Ipomoea aquatica, Ipomoea cairica, Ipomoea nil, Ipomoea triloba, and Ipomoea trifida, respectively. Phylogenetic analysis categorized the GATA genes into six groups according to their distinct features, and this classification was validated by the structural characteristics of exons/introns and conserved motif analysis. The cis-acting elements located in the promoter regions were also found to be enriched with biotic and abiotic responsive elements, which may play a pivotal role in plant stress adaptation. Then the gene duplication events and synteny between the genome of sweet potato and those of Ipomoea aquatica, Ipomoea cairica, Ipomoea nil, Ipomoea triloba, and Ipomoea trifida were analyzed, which provided insights into evolutionary mechanisms. Moreover, expression pattern analysis was performed on IbGATA genes, many of which were significantly induced by multiple types of abiotic stress, which may render these genes candidates for molecular breeding strategies in sweet potato. Overall, this experiment conducted a systematic exploration of GATA genes by investigating their evolutionary relationships, structural characteristics, functional properties, and expression patterns, thereby establishing a theoretical foundation for further in-depth research on the features of the GATA gene family.

Keywords: GATA transcription factor; abiotic stress; drought and salt stress; genome-wide; sweet potato (Ipomoea batatas L.).

FIGURE 1

Phylogenetic tree of GATA genes in I. batatas, I. aquatica, I. cairica, I. nil, I. triloba, I. trifida, Arabidopsis thaliana, and Oryza sativa.

FIGURE 2

Evolutionary relationship, conserved motifs, protein conserved domains, and gene structure of GATA proteins in Ipomoea species. (A–F) I. batatas, I. aquatica, I. cairica, I. nil, I. triloba, and I. trifida.

FIGURE 3

Chromosome localization of GATA genes in Ipomoea species. (A–F) Ipomoea batatas, I. aquatica, I. cairica, I. nil, I. triloba, and I. trifida.

FIGURE 4

Cis-acting elements in the promoters of IbGATA genes in I. batatas.

FIGURE 5

Collinearity analysis of the GATA genes between Ipomoea species. (A) Ipomoea batatas and I. aquatica; (B) Ipomoea batatas and I. cairica; (C) Ipomoea batatas and I. nil; (D) Ipomoea batatas and I. triloba; (E) Ipomoea batatas and I. trifida. (F) Schematic representation of syntenic genes among I. batatas, I. aquatica, I. cairica, I. nil, I. triloba, and I. trifida.

FIGURE 6

Schematic diagram of GATA gene collinearity analysis in Ipomoea species. (A–F) I. batatas, I. aquatica, I. cairica, I. nil, I. triloba, and I. trifida.

FIGURE 7

The expression profile of the IbGATA gene in sweet potato was detected through qRT-PCR. (A) Relative gene expression levels in different tissues: root, stem, leaf, and petiole. (B) Relative gene expression levels under drought (20% PEG-6000) treatment over the same time periods (0, 6, 12, and 24 h). The control group was treated with distilled water. (C) Relative gene expression levels under salt (200 mM NaCl) treatment over the same time periods (0, 6, 12, and 24 h). Data represent the mean of three biological replicates ±SD (n = 3). Error lines indicate standard deviations. Different lowercase letters (a, b, c, and d) on the bars indicate significant differences at p < 0.01.