Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat (Triticum aestivum)

Abstract

Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat.

Keywords: RT-qPCR; bioinformatics; cis-element; expression profiling; gene structure; miRNA; subcellular localization.

Figure 1

Phylogenetic tree of the DUF724 proteins from three species. Ten Arabidopsis thaliana, five Oryza sativa and fourteen Triticum aestivum. Different-colored circles represent different species.

Figure 2

Chromosome localization, collinearity analysis and Ka/Ks analysis of TaDUF724 genes. (A) Chromosome distribution of TaDUF724s. Chr stands for chromosome. The scale on the left represents the physical length of chromosome (Mbp). (B) Collinearity analysis diagram of TaDUF724s. (C) Ka and Ks scatter diagram of DUF724 homolog gene pairs among wheat and different species.

Figure 3

Phylogenetic tree, gene structure and conserved Motif of TaDUF724s. (A) Phylogenetic tree of TaDUF724s. (B) Gene structure of TaDUF724s, green represents CDS, yellow represents UTR and black lines represent introns. (C) Motif distribution of TaDUF724s, different colors represent different Motifs.

Figure 4

Predicted 3D models of TaDUF724s. Models were generated by using SWISS-MODEL.

Figure 5

Statistical analysis of cis-acting elements of TaDUF724 promoters. The color and number of grids represent the number of cis-acting elements in the corresponding TaDUF724s.

Figure 6

Expression patterns of TaDUF724s during growth and development, biological and abiotic stress treatments. The log2 (transcripts per kilobase of exon model per million mapped reads + 1) values were used to draw the heatmap. Zt stands for Zymoseptoria tritici and Sr stands for stripe rust.

Figure 7

Sankey diagram for the relationships of miRNA targeting to TaDUF724 transcripts. The three columns represent miRNA, TaDUF724s and inhibition effect.

Figure 8

RT-qPCR expression analysis of six selected TaDUF724 genes in response to (A) PEG, (B) NaCl, (C) F. graminearum and (D) P. striiformis. Different colors represent different treatments. Vertical bars indicate the standard error of the mean, and different letters are significantly different (t-test, p < 0.05).