Transcriptome analysis of <i>CsWOX1</i> mutant and overexpressing lines reveals downstream genes regulating cucumber leaf morphogenesis

<i>WUSCHEL-related homeobox 1</i> (<i>WOX1</i>), categorized into the WUS clade, has been determined as the essential gene for leaf expansion as well as promoting leaf outgrowth along the mediolateral axis. The phenotypic characteristics of transgenic cucumber plants with <i>CsWOX1</i> overexpression (<i>CsWOX1</i>-OE) and mutants (designated as <i>mango fruit</i>, <i>mf</i>) have been reported. Specifically, <i>CsWOX1</i>-OE cucumber plants exhibit leaves with a distinctive 'butterfly-shaped' appearance, while <i>mf</i> mutants show a rapid reduction in the area of their leaf tips. In this study, RNA-Seq was employed to sequence the transcriptome of <i>CsWOX1</i>-OE to reveal its differentially expressed genes (DEGs). Combined with the transcriptome sequencing data of the <i>mf</i> mutant, GO classification, and KEGG pathway enrichment analyses were performed, revealing new links between the WOX1 protein and many core plant regulatory pathways. The further joint analysis identified 80 common DEGs between <i>CsWOX1</i>-OE and <i>mf</i>, with a significant proportion of these common DEGs being annotated to the circadian pathway and the auxin polarity transport pathway. Six genes (<i>CsGI</i>, <i>CsFKF1</i>, <i>CsRVE6</i>, <i>CsRVE8</i>, <i>CsABCB,</i> and <i>CsPin1At</i>) were selected for Y1H and Dual-LUC interaction validation experiments. These experiments demonstrated that <i>CsWOX1</i> directly targets the promoters of <i>CsRVE6</i>, which regulates leaf expansion, and <i>CsPin1At</i>, which is involved in auxin polarity transport, thereby promoting their transcription. In conclusion, these findings provide a foundation for exploring the potential regulatory mechanisms associated with <i>CsWOX1</i>, expecting to contribute to the construction of a more comprehensive gene network for leaf morphogenesis.