Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max)

Soybean possesses 19 CMF genes which mainly arose from duplication events. Their features and motifs are highly conserved but transcriptional data indicated functional diversity in metabolism and stress responses. CCT [for CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)] domain-containing genes play important roles in regulating flowering, plant growth, and grain yield and are also involved in stress responses. The CMF (CCT motif family) genes, included in the CCT family, contain a single CCT domain as the only identifiable domain in their predicted protein sequence and are interesting targets for breeding programs. In this study, we identified 19 putative GmCMF genes, based on the latest soybean (Glycine max) genome annotation. The predicted GmCMF proteins were characterized based on conserved structural features, and a phylogenetic tree was constructed including all CMF proteins from rice and Arabidopsis as representative examples of the monocotyledonous (monocot) and dicotyledonous (dicot) plants, respectively. High similarities in the conserved motifs of the protein sequences and the gene structures were found. In addition, by analyzing the CMF gene family in soybean, we identified seven pairs of genes that originated from segmental chromosomal duplication events attributable to the most recent whole-genome duplication (WGD) event in the Glycine lineage. Expression analysis of GmCMF genes in various tissues and after specific treatments demonstrated tissue and stress-response specific differential expression. Gene expression analysis was complemented by the identification of putative cis-elements present in the promoter regions of the genes through a bioinformatics approach, using the existing soybean reference genome sequence and gene models. Co-functional networks inferred from distinct types of genomics data-including microarrays and RNA-seq samples from soybean-revealed that GmCMF genes might play crucial roles in metabolism and transport processes. The results of this study, the first systematic analysis of the soybean CCT gene family, can serve as a strong foundation for further elucidation of their physiological functions and biological roles.