Abstract
Prokaryotic and viral genomes evolve rapidly by high mutation rates and frequent genomic structural changes, including recombination, gene gain/loss and genome rearrangement. However, whether and how genomic structural alterations might influence the substitution rates of prokaryotic genes remains underexplored. In Chapter 2, we examine the correlations between evolutionary rates and changes in transcriptional orientation in enterobacterial genomes. Our results indicate that changed-orientation genes (ChOGs) have significantly higher rates of synonymous (dS) and non-synonymous (dN) substitutions but similar dN/dS ratios as compared with same-orientation genes (SOGs). The correlations are not confounded by gene essentiality, gene expression level, replication-transcription confrontation, or genomic location. These observations suggest that the increases in evolutionary rates in ChOGs may be mainly mutation-driven instead of selection-driven. In Chapter 3, we aim to investigate the effects of genomic recombination on the evolution of viral genes. As the first step, we develop a web-based tool for Enterovirus (EV) genotyping and recombination detection named EVIDENCE (Enterovirus in deep conception). Additionally, to avoid potential mistyping, we introduce the “mixed–ranking scores” to evaluate the fitness of prototypes by the relatedness and by the genome regions of interest. The mixed-ranking scores which sum up the rank of three parameters in BLAST result, including identity, query coverage and bit-score, were used in genotype re-classification and the first step of novel sequence genotyping to overcome inherent disadvantage for using each of them alone. This platform can facilitate future studies in EV evolution.