Genome evolutionary studies of the Salmonella enterica serovars: implications for the dynamics of horizontal gene transfer, the pangenome concept, and bacterial and archaeal taxonomy

With the vast expansion of complete microbial genome sequences, it is increasingly apparent that the genomes of free-living and facultative microbes living in competitive environments are astonishingly dynamic. That is, such microbes appear to be constantly subjected to gene gain and gene loss processes. The influence of gene gain, specifically through the process of horizontal gene transfer, appears to be so profound that the gene content amongst strains of a lineage may vary as much as 80%. However, the sources of horizontal gene transfer and its overall dynamics have remained elusive, despite increasing whole genome sequence diversity. The vast extent of genetic variability in some lineages is at the heart of a complex debate in microbial taxonomy, including as to if a species concept is even possible for microbes. Gene loss also plays a significant role in the evolution of microbial genomes. If free-living and facultative organisms are constantly subject to gene gain via horizontal gene transfer, then their finite genome sizes indicate that the gene gain must be balanced by gene loss. Though genes can be lost outright, it was apparent at the outset of these studies that another readily detectable form of gene loss, pseudogene formation, was an increasingly important mode of loss within microbes. This dissertation describes our analyses of the horizontally acquired genes and pseudogene accumulation in the Salmonella enterica serovars. The wide range of diseases amongst a wide range of hosts elicited by the S. enterica serovars suggests that they have a diverse complement of presumably horizontally acquired genes that contribute to their unique virulence traits. Further, the initial S. enterica serovar genome sequences revealed that a broad host range serovar had far fewer pseudogenes than that of a narrow host range serovar. In combination with the fact that much is known about the S. enterica serovars, this lineage provides an ideal system in which to study the evolutionary dynamics of gene gain and gene loss processes. Chapters 2 and 3 describe the codon usage studies of the horizontally acquired genes of S .enterica. Chapter 2 provides the first known quantitative evidence that some groups of closely related, but traditionally distinct species derive the plurality of their recently horizontally acquired genes from a common accessory gene pool. We refer to this phenomenon as the supraspecies pangenome. We also demonstrate that supraspecies pangenomes are widespread across the microbial world; they are found amongst other bacterial lineages and even archaeal lineages. Further, since these genes pools are shared beyond the species level implies that this phenomenon has significant implications for microbial taxonomy. Whereas our studies in Chapter 2 focus on the ancestral and most recently acquired genes, we expand our studies of horizontally transferred genes in Chapter 3. Specifically, we incorporate the accessory supraspecies pangenome codon usage found in Chapter 2 to analyze intermediate evolutionary classes of genes, such as species-specific genes. This allows us to ask questions about the fates of horizontally acquired genes, particularly in view of the current assumptions about them. In doing so, we find that the codon usages of many anciently acquired genes, including many important genomic islands, are similar to the codon usages of the most recently acquired genes of the accessory supraspecies pangenome. These findings challenge the dogma on the fate of horizontally acquired genes, and ultimately lead us to the proposal of that some microbial lineages maintain a secondary stress-related intrinsic codon usage. Chapter 4 describes our studies on pseudogene accumulation in the S. enterica serovars. The initial project objectives included the sequencing and comparative analysis of several S. enterica serovar genomes, with the hypothesis that pseudogene accumulation would be more profound in narrow host range serovars as compared to broader host range serovars. These sequencing projects ultimately transitioned to other institutions that published their analyses of the sequences including their observations on pseudogene accumulation relative to host range. I compile these published findings to confirm our original hypothesis. I also provide a detailed codon usage analysis of a genomic region that appears to a hot spot of pseudogene accumulation in the host-specific S. enterica serovars relative to the broader host range serovars. Surprisingly, although the overall function of this pathway has been lost amongst the host-specific serovars, some genes in this region have signatures of conservation, suggesting that they have some ancillary function in the host-specific setting. Our analyses of the horizontally acquired genes and pseudogene accumulation in the S. enterica serovars have several significant implications on the understanding of the microbial genome and its evolutionary dynamics. I will discuss how these findings challenge some of the current paradigms and dogma regarding the dynamics of horizontal gene transfer, the fate of horizontally transferred genes, the pangenome concept, and the definition of bacterial and archaeal species