Integrative evolutionary and structural modeling of leaf rust resistance genes in wheat (Triticum aestivum subsp. and T. monococcum).

This study investigated the evolutionary relationships and molecular characteristics of selected genes in wheat (Triticum aestivum subsp.) using phylogenetic reconstruction and motif analysis. A phylogenetic tree was constructed using the Maximum Likelihood method, and conserved motif patterns were identified using ClustalW alignment and R-based analyses. The detection of a shared conserved motif across genes G3 to G11 at the same position suggests functional conservation, shared regulatory roles, or evolutionary constraint. Highly significant motifs identified in Gen1 and Gen2 indicate potential functional importance, possibly corresponding to active or binding sites. Phylogenetic analysis grouped the genes into two main clusters; a strongly supported monophyletic clade (Gen1, Gen10) suggests conserved functional roles, whereas weaker support among Gen13-Gen18 limits resolution of deeper evolutionary relationships. Sequence logo analysis revealed conserved regions between positions 107 and 301, particularly at residues P, L, R, F, G, and K, while positions 200-260 exhibited low conservation, indicating potential functional divergence. Structural prediction using AlphaFold2 revealed a canonical ABC transporter fold with high-confidence nucleotide-binding domains and a membrane-spanning helical bundle containing conserved catalytic residues, supporting an ATP-dependent transport function in wheat. Overall, these findings provide insights into the evolutionary history, structural conservation, and potential functional roles of these genes in wheat.