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

The yellow flower lotus (<i>Nelumbo lutea</i>) is the sister species of the sacred lotus (<i>N. nucifera</i>). The evolution of gene expression patterns across multiple tissues during the species divergence of these two lotuses remains unexplored. The WUSCHEL-related homeobox (<i>WOX</i>) 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 <i>NlWOX</i> genes into three subfamilies. We identified seven syntenic gene pairs between <i>NnWOX</i>s and <i>NlWOX</i>s that originated from whole-genome duplications. Through conserved motif analysis, we found subfamily-specific motifs in the protein sequences of <i>NnWOX</i>s and <i>NlWOX</i>s. Variations in the three-dimensional conformations of homologous <i>WOX</i> genes indicate function divergences between the two lotus species. The gene expression matrix of <i>NlWOX</i> across tissues reveals expression divergences within <i>N. lutea</i> and between the two lotus species. By employing a weight gene co-expression network analysis pipeline, we developed eight <i>NlWOX</i> co-expression networks that differed from the co-expression networks of their syntenic genes. Overall, our findings suggest that genomic variations in the <i>WOX</i> orthologs contribute to the distinct expression patterns and regulatory networks observed during the evolution of these two lotuses.