The Tissue Expression Divergence of the WUSCHEL-Related Homeobox Gene Family in the Evolution of Nelumbo.

The yellow flower lotus () is the sister species of the sacred lotus (). The evolution of gene expression patterns across multiple tissues during the species divergence of these two lotuses remains unexplored. The WUSCHEL-related homeobox () family, a plant-specific transcription factor family, plays a crucial role in tissue development and stress responses. In this study, utilizing a chromosome-level reference genome and a transcriptome database covering multiple tissues, we identified and categorized 11 genes into three subfamilies. We identified seven syntenic gene pairs between s and s that originated from whole-genome duplications. Through conserved motif analysis, we found subfamily-specific motifs in the protein sequences of s and s. Variations in the three-dimensional conformations of homologous genes indicate function divergences between the two lotus species. The gene expression matrix of across tissues reveals expression divergences within and between the two lotus species. By employing a weight gene co-expression network analysis pipeline, we developed eight co-expression networks that differed from the co-expression networks of their syntenic genes. Overall, our findings suggest that genomic variations in the orthologs contribute to the distinct expression patterns and regulatory networks observed during the evolution of these two lotuses.