| Summary: | WUSCHEL-related homeobox (<i>WOX</i>) genes are a class of plant-specific transcription factors, regulating the development of multiple tissues. However, the genomic characterizations and expression patterns of WOX genes have not been analyzed in lotus. In this study, 15 <i>NnWOX</i> genes were identified based on the well-annotated reference genome of lotus. According to the phylogenetic analysis, the <i>NnWOX</i> genes were clustered into three clades, i.e., ancient clade, intermediate clade, and WUS clade. Except for the conserved homeobox motif, we further found specific motifs of <i>NnWOX</i> genes in different clades and divergence gene structures, suggesting their distinct functions. In addition, two <i>NnWOX</i> genes in the ancient clade have conserved expression patterns and other <i>NnWOX</i> genes exhibit different expression patterns in lotus tissues, suggesting a low level of functional redundancy in lotus <i>WOX</i> genes. Furthermore, we constructed the gene co-expression networks for each <i>NnWOX</i> gene. Based on weighted gene co-expression network analysis (WGCNA), ten <i>NnWOX</i> genes and their co-expressed genes were assigned to the modules that were significantly related to the cotyledon and seed coat. We further performed RT-qPCR experiments, validating the expression levels of ten <i>NnWOX</i> genes in the co-expression networks. Our study reveals comprehensive genomic features of <i>NnWOX</i> genes in lotus, providing a solid basis for further function studies.
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