Fig 1.
Phylogenetic analysis of CCT proteins in wheat, Arabidopsis, Brachypodium, and rice.
The CCT proteins were phylogenetically analyzed using MEGA v6.0 following the UPGMA method. The proteins from different plants are represented in different colored squares (wheat, red; Arabidopsis, green; Brachypodium, yellow; rice, blue). The gene IDs are listed in S1 and S2 Tables.
Fig 2.
Phylogenetic analysis, conserved motif and structure analysis of CCT genes in wheat.
The motifs and conserved domains were predicted using the MEME suite and the Batch CD-Search tool, respectively, and displayed using TBtools. Phylogenetic analysis of the proteins was performed using MEGA v6.0 following the UPGMA method.
Fig 3.
WebLogo representation of the conserved CCT domain.
Black asterisks indicate identical residues in all CCT domains, and red asterisks indicate identical residues in most CCT domains. The black arrow indicates the residue insertion of PL before L17 in TaCMF7. Triangles with numbers representing the corresponding phylogenetic classification groups suggest the splitting site of the motif.
Fig 4.
Chromosomal localization of CCT genes in wheat visualized by TBtools.
Gene clusters with at least three genes distributed among the three subgenomes are marked on the right. Asterisks indicate the clusters with tandemly arranged genes, and the copy number in each subgenome is shown in parentheses.
Fig 5.
Expression profiling of CCT genes in wheat before, during, and after vernalization by RNA sequencing.
The leaf samples were harvested before vernalization (v0), after one week’s vernalization (v1), two weeks’ vernalization (v2), three weeks’ vernalization (v3), four weeks’ vernalization (v4), five weeks’ vernalization (v5), six weeks’ vernalization (v6), and one-week normal growth after six weeks’ vernalization (pv1). The phylogenetic analysis that appeared here was the same as that in Fig 2.
Fig 6.
UpSet plot diagram of upregulated and downregulated CCT genes during/after vernalization compared with pre-vernalization.
A: Upregulated genes; B: Downregulated genes. The leaf samples were harvested the same as those in Fig 5. Transcriptome sequencing was conducted to obtain the gene expression data, which was expressed as FPKM.
Fig 7.
Expression profiling of CCT clusters using quantitative real-time PCR in wheat before, during, and after vernalization.
The leaf samples were harvested the same as those in Fig 5. The expression level of each cluster before vernalization was used as the standard, and the relative gene expression levels during and after vernalization were calculated using the 2-ΔΔCT method. The expression of CCT clusters was normalized to the housekeeping gene TaActin. Three biological replicates were maintained for each sample, and the deviations in gene expression level were indicated by standard error (SE).