Genome-Wide Reidentification and Transcriptome Analysis of Mads-Box Gene Family in Cucumber

MADS-box transcription factors play an important role in plant growth and development. Although previous studies have carried out genome-wide analysis of the MADS-box family in cucumber, with the update of the genome data of Cucurbitaceae, this paper re-identified and analyzed the differences of the family genes in different genome versions. The results showed that a total of 48 CsMADS-box genes were identified in the V3 version of cucumber, while three of the 43 genes identified in the V1 version were duplicated. The V1 version actually has only 40 genes. Additionally, we analyzed the variability in protein sequences and found that the amino acid sequences of 14 genes showed no differences between the two versions of the database, while the amino acid sequences of 29 genes exhibited significant differences. Further analysis of conserved motifs revealed that although the amino acid lengths of 15 genes had changed, their conserved motifs remained unchanged; however, the conserved motifs of 12 genes had altered. Furthermore we found that motif1 and motif2 were present in most proteins, indicating that they are highly conserved. Gene structure analysis revealed that most type I (Mα, Mβ) MADS-box genes lack introns, whereas type II (MIKC) genes exhibit a similar structure with a higher number of introns. Chromosomal localization analysis indicated that CsMADS-box genes are unevenly distributed across the seven chromosomes of cucumber. Promoter region analysis showed that the promoter regions of CsMADS-box genes contain response elements related to plant growth and development, suggesting that CsMADS-box genes may be extensively involved in plant growth and development. Different CsMADS-box genes exhibit specific high expression in roots, stems, leaves, tendrils, male flowers, female flowers, and ovaries, suggesting that these genes play crucial roles in the growth, development, and morphogenesis of cucumber. Moreover, 26, 18, 8, and 10 CsMADS-box genes were differentially expressed under high temperature, NaCl and/or silicon, downy mildew, and powdery mildew treatments, respectively. Interestingly, CsMADS07 and CsMADS16 responded to all tested stress conditions. These findings provide a reference and basis for further investigation into the function and mechanisms of the MADS-box genes for resistance breeding in cucumber.