Genome-Wide Identification and Expression Analysis of NF-Y Transcription Factor Families in Watermelon (Citrullus lanatus)

Nuclear factor Y (NF-Y) proteins are heterotrimeric transcription factors composed of NF-YA, NF-YB, and NF-YC subunits. These proteins play crucial roles in regulating plant growth, development, and abiotic and biotic stress responses. However, little is known about NF-Y genes in watermelon (Citrullus lanatus). The recent publication of the draft genome of watermelon has allowed for a more comprehensive analysis of NF-Y genes in this species. In this study, a total of 19 ClNF-Y genes, including 7 ClNF-YA, 8 ClNF-YB, and 4 ClNF-YC genes, were identified in the watermelon genome. Gene structure analysis suggested that exon/intron structures were conserved within subgroups but differed between subgroups in the ClNF-Y family. Chromosomal distribution mapping showed that the 19 ClNF-Y genes were unevenly located on nine chromosomes in the watermelon genome. Conserved domain analysis and multiple alignments demonstrated that ClNF-Y proteins share the same conserved domains as those in Arabidopsis and mouse. Phylogenetic analysis revealed that Cucurbitaceae NF-Y proteins are more closely related to the Arabidopsis homologs than to the rice OsNF-Y proteins. Expression pattern analysis by quantitative real-time PCR indicated that all ClNF-Y genes were actively expressed in six evaluated watermelon tissues, with significantly higher expression in leaves and roots. Among the 19 ClNF-Y genes, the expression of 13, including 5 ClNF-YA, 5 ClNF-YB, and 3 ClNF-YC genes, significantly changed upon exposure to salt and drought stresses, suggesting that these 13 ClNF-Y genes might be involved in the response to salt and drought stresses in watermelon. Thus, this study provides a solid foundation for further functional analysis of NF-Y proteins during watermelon development and responses to salt and drought stresses. Furthermore, the results will be valuable for evolutionary analysis of the NF-Y family in Cucurbitaceae species.