Genome-Wide Identification and Expression Profiling Analysis of the CCT Gene Family in Solanum lycopersicum and Solanum melongena

CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in <i>Solanum</i> species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family in two <i>Solanum</i> species: tomato (<i>Solanum lycopersicum</i> L.) and eggplant (<i>Solanum melongena</i> L.). A total of 27 <i>SlCCT</i> and 29 <i>SmCCT</i> genes were identified in the tomato and eggplant genomes, respectively. Phylogenetic analysis showed that the CCT gene family could be divided into six subgroups (COL I, COL II, COL III, PRR, CMF I, and CMF II) in <i>Oryza sativa</i> and <i>Arabidopsis thaliana</i>. The similarity in the distribution of exon-intron structures and conserved motifs within the same subgroup indicated the conservation of <i>SlCCT</i> and <i>SmCCT</i> genes during evolution. Intraspecies collinearity analysis revealed that six pairs of <i>SlCCT</i> genes and seven pairs of <i>SmCCT</i> genes showed collinear relationships, suggesting that segmental duplication played a vital role in the expansion of the <i>SlCCT</i> and <i>SmCCT</i> family genes. <i>Cis</i>-acting element prediction indicated that <i>SlCCT</i> and <i>SmCCT</i> were likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. RT-qPCR analysis revealed that <i>SmCCT15, SlCCT6/SlCCT14</i>, and <i>SlCCT23/SmCCT9</i> responded significantly to salt, drought, and cold stress, respectively. Our comprehensive analysis of the CCT gene family in tomato and eggplant provides a basis for further studies on its molecular role in regulating flowering and resistance to abiotic stress, and provides valuable candidate gene resources for tomato and eggplant molecular breeding.