BackgroundKinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions has not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear.ResultsIn this study, we performed a whole-genome search and comprehensive analysis in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by chromosomal distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which explains the expansion of the kinesin gene family in C. lanatus genome. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, indicating their critical regulatory roles during early fruit development. Our current data also demonstrated that the majority of kinesin genes were responsive to plant hormones, implying their involvement in the signaling pathways of plant hormones.ConclusionsThis study is the first comprehensive analysis of the kinesin gene family in watermelon, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results will provide a useful resource for further selecting an artificial regulator of fruit development in C. lanatus.