Bioinformatics Genome-Wide Characterization of the WRKY Gene Family in Sorghum bicolor

The WRKY gene family encodes a large group of transcription factors that regulate genes involved in plant response to biotic and abiotic stresses. Sorghum is a notable grain and forage crop in semi-arid regions because of its unusual tolerance against hot and dry environments. In this study, we performed a genome-wide analysis of WRKYs using a genome assembly of sorghum bicolor. First, all possible WRKY gene sequences as well as all possible WRKY protein sequences in the Sorghum bicolor genome database were identified using the NCBI website. A set of 85 WRKY genes was identified in the S. bicolor genome and classified into three groups (I–III). Among the members of the group I, the SbWRKY13 had a different and novel zinc finger motif as compared to other members of this group. It was also found that mutations occurred at R, K, Y and Q in the conserved WRKYGQK sequence. No complete gene duplication was found in gene copy number investigation, suggesting that the expansion of SbWRKY genes was not necessarily based on the gene duplication events or duplication of SbWRKY genes had probably happened in the past times. Gene cluster analysis showed that the number of genes on chromosomes were positively correlated with the number of clusters. The study of amino acid composition revealed that totally in all groups, Alanine and Proline were the most frequent residues while Cysteine had the lowest frequency. The study of introns in the SbWRKY domain showed that the majority of SbWRKY genes had two types of introns in their WRKY domains (phase 0 and phase 2). Also, investigation of conserved known motifs revealed that there were six, two and one known motifs outside of the region of the SbWRKY domain for groups IIa, IIb and IIc, respectively. The results describe evolution and functional differentiations of WRKY transcription factors in Sorghum bicolor.