Evolution of Salmonella Chromosomes and Its Influence on Gene Expression and Chromosomal Topology

Salmonella is an important bacterial pathogen, containing ~2,600 serovars. It remains unclear how the genomes have evolved as Salmonella species, subspecies and serovars differentiate. To investigate the evolution of Salmonella chromosomes and their consequence, we collected the complete genomes of representative strains of each Salmonella species and subspecies, inferred the gene composition and order in the ancient orthologous chromosomes, and delineated their evolutionary trajectory and gene flow. Generally, the ancient orthologous chromosomes show low plasticity, and more rearrangement events happened in a locus-specific way rather than spontaneously within chromosomes. The rearranged genes are mainly involved in iron transport and metabolism, virulence and fimbriae biosynthesis. Although the effects may be lower than those produced by bacterial growth-phase shifting, RNA sequencing analysis demonstrates that genetic rearrangements do influence the expression of background genes located in the ancient chromosomal blocks in a manner related to distance-from-breakpoint and rearrangement-scale. High-resolution chromosome conformation capture (Hi-C) sequencing experiments were performed on representative Salmonella strains. The general chromosomal conformation is conserved among the Salmonella species and subspecies and consistent with Escherichia coli, with only a single strong DNA contact diagonal and six macrodomains. The number and boundaries of chromosomal interaction domains (CIDs) vary among the Salmonella strains, which are largely influenced by the genomic rearrangements. Interaction analysis revealed a list of significant long-range intra-chromosome contacts involving functionally enriched genes, similar to the frequently rearranged genes. Taken together, the study provides a comprehensive survey of Salmonella chromosomes evolution, and a systematic observation of direct and indirect effects on chromosomal topology, inter-chromosomal interaction and gene expression.