Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

Abstract

Background: Of the > 2000 serovars of Salmonella enterica subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, S. enterica serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi.

Results: We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2) identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes.

Conclusion: Recombination and pseudogene-formation have been important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in Salmonella.

Figure 1

Tandem repeats in the O-antigen biosynthesis cluster in Paratyphi A ATCC9150. Bottom row: gene arrangement in Paratyphi A AKU_12601 and Typhi, presumed to be the ancestral form. Top row: gene arrangement in Paratyphi A ATCC9150, apparently resulting from two tandem duplications. Labels give systematic identifiers for the gene sequences in each genome, identical coding sequences are shown in the same colours, identical sequences are joined by lines.

Figure 2

Scenarios of recombination and pseudogene formation in Paratyphi A and Typhi. (a) True distribution of pseudogenes in the Paratyphi A AKU_12601 and Typhi CT18 genomes (gene order based on gene co-ordinates in Typhi CT18). (b-c) Distribution of pseudogenes resulting from data simulated under two scenarios, under both of which 40 pseudogenes are inherited from the most recent common ancestor of Paratyphi A and Typhi, and extensive accumulation of pseudogenes occurs before or after recombination of 25% of genes. For ease of simulation, the recombination shown is uni-directional, but bi-directional exchange would result in similar patterns. (b) Scenario 1: 150 additional pseudogenes accumulate in each serovar, followed by recombination. (c) Scenario 2: only 20 additional pseudogenes arise before recombination, after which a further 150 pseudogenes accumulate in each serovar.

Figure 3

Pseudogene formation in the evolutionary histories of Paratyphi A and Typhi. Phylogenetic tree based on multiple alignments of all nonrecombined genes as defined in [15], rooted using S. bongori and E. coli as outgroups. Scale bar is nucleotide divergence. The timing of the recombination between Paratyphi A and Typhi is an approximation inferred from published divergence data [15]. Group (i) pseudogenes were inactivated prior to the divergence of Paratyphi A and Typhi, some are also inactivated in Typhimurium and Paratyphi B; following their divergence Paratyphi A and Typhi likely accumulated few additional pseudogenes; during the recombination of 23% of their genomes (direction of transfer unknown) 18 pseudogene sequences were shared between Paratyphi A and Typhi, including five non-ancestral pseudogenes (group ii); many pseudogenes were formed during a period of accelerated pseudogene accumulation in both serovars, including most group (iii) pseudogenes; pseudogenes continue to accumulate in individual sub-lineages after the most recent common ancestor of each serovar (group iv).