Evolutionary Analysis Of F-box Gene Family In Saccharomycetaceae

As a core component of Skp1-Cul1-F-box(SCF) ubiquitin ligase complexes, the F-box protein is involved in various cellular processes in yeasts, such as DNA replication, regulation of the cell cycle, and mating type switching. However, most previous works were mainly focused on the evolutionary pattern of F-box genes in plants and Euarchontoglires, and the knowledge of the evolution of the F-box gene family in yeasts is limited. In this study, we investigated F-box gene number variation and underlying mechanisms, selection patterns and intramolecular coevolution during evolution of yeasts, all of which are benefit to deeply understand genome evolution and figure out the function of the F-box proteins. We investigated the F-box genes in ten of the related yeast species in Saccharomycetaceae, and the main results are as follows:1. All the protein sequences from the ten strains were checked to identify the domain architectures by the InterProScan software. A total of 136 protein-coding F-box genes were identified in ten genomes. In addition to the F-box domain, six other domains were identified in these F-box proteins.2. Based on phylogenetic relationships, all the F-box genes were clustered into 20 orthogroups. The proteins in each orthogroup had the same domain structure, and the Lineage-specific domain gain and loss events did not occur.3. The evolutionary history of F-box gene numbers in 10 Saccharomycetaceae yeasts was reconstructed. Although the changes in the total numbers of F-box genes among the 10 yeast species was unconspicuous, whole genome duplication, interspersed repeats and lots of gene loss events were still discovered. However the whole genome duplication did not make a contribution to the growth of the copies of F-box genes. The mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes.4. Sixty-nine and fourteen positive selected sites were detected in F-box proteins in program Selecton and datamonkey web-server, respectively. But only twenty six positive selected sites had changed radically in amino acid properties by using TreeSAAP. The results indicated that the evaluation of selective pressures solely at the nucleotide level could be misleading.5. Fifty-nine groups of coevolutionary residues were detected in intramolecular coevolutionary analysis using CAPS software. Fifteen groups were only significantly correlated with the hydrophobicity(P < 0.05), and twelve groups were only significantly correlated with the molecular weight(P < 0.05). Fourteen groups were significantly correlated with the hydrophobicity and molecular weight(P < 0.05).