Evolutionary Analysis and Functional Identification of Clock-Associated () Genes in the Flowering Regulation of Roses.

Pseudo-response regulators () are the important genes for flowering in roses. In this work, clock were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock were significantly expanded in Rosaceae and were divided into three major clades, i.e., (clade 1), (clade 2), and (clade 3), based on their phylogeny. Within the clades, five clock were identified in . Clock had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock . The diverse cis elements and interaction of clock with suggested their role in plant development. Co-expression network analysis showed that the clock from had a strong association with flowering controlling genes. Further silencing of and in using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between / and suggested that / may suppress flowering by interfering with the binding of to the promoter of . Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock in controlling flowering in roses.