PJB-2025-301
Genome-Wide Identification and Characterization of the WRKY Gene Family in White Fonio
BAO-LIN HAN
Abstract
White fonio (Digitaria exilis), a traditional West African cereal, exhibits valuable agronomic traits including a short growth cycle and pronounced drought tolerance. However, researchers have poorly characterized its molecular biology, especially regarding key regulatory gene families such as WRKY transcription factors. This study systematically identified and analyzed the WRKY gene family in D. exilis to clarify its potential role in stress adaptation. We screened the complete D. exilis genome using BLASTP and HMMER, identifying 112 non-redundant DeWRKY genes. Our comprehensive bioinformatic analyses encompassed phylogenetic classification, chromosomal localization, examination of conserved motifs and gene structures, prediction of cis-acting elements, and collinearity assessment. Unevenly distributed across 18 chromosomes, the 112 DeWRKY genes fall into phylogenetic Groups I, II, and III, with Group II constituting the largest clade (44%). This phylogenetic profile aligns with the structure observed in model plants such as Arabidopsis thaliana. Conserved motif analysis detected Motif 1 (the WRKY domain) in all members, with Motif 2 and Motif 4 also appearing frequently. Promoter analysis uncovered abundant cis-elements for stress and hormone responses, especially those involved in drought and abscisic acid signaling. Intra-genomic collinearity analysis highlighted the major contribution of segmental duplications to the expansion of the DeWRKY family. In summary, this work presents the first genome-wide characterization of the WRKY family in D. exilis, addressing a notable knowledge gap. Our findings provide important insights into the genomic architecture and potential regulatory functions of DeWRKY genes in environmental stress responses, thereby establishing a theoretical basis for future functional studies and molecular breeding programs targeting enhanced stress tolerance in crops.
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