Evolutionary genomics of Salmonella enterica subspecies

This post will be a short summary of an interesting paper by Michael McClelland’s group, Evolutionary genomics of Salmonella enterica subspecies, Desai et al., 2011. I will focus on the phylogenetic aspects of the study as this is my primary interest at the moment.

Intro

  • 6 sub-species of Salmonella enterica, 5/6 of which (excluding enterica subsp enterica) are primarily isolated from cold blooded animals.
  • 99% of human Salmonella infections caused by 50 of the 2600 Salmonella serovars – all 50 of these are in Salmonella enterica Subsp enterica

Study aim

  • They sequenced 21 Salmonella, 11 diverse subsp enterica, 2 from each of the other subspecies (which had no sequenced representatives prior to this).
  • Test phylogenetic hypotheses and gene family presence/absence.

Methods highlights

  • Whole genome alignments of assembled genomes (454+newbler) and SNPs called using S. Typhimurium LT2 (subspecies enterica) as ref. They seem to have used Mauve to call SNPs, not sure how this works exactly…
  • Recombination analysis of orthologous regions (how could they tell this before they had done the recombination analysis?) conserved across all genomes and at least 10 kb in length were analysed using clonal frame. Only 104 kb of the genome met their criteria!

Results and discussion highlights

  • They are upfront about the limits of draft genomes.
  • Identified 737062 SNPs in a Salmonella enterica core genome of 2.6 Mb – seems at odds with their figure of 104 kb above?
  • They used a variety of phylogenetic methods to increase the strength of their conclusions.
  • They say that Salmonella genomes undergo frequent intergenomic recombinations. Their clonal frame analysis of 4% of the core genome revealed an r/m of 0.94, and the recombination detection program suggested hundreds of recombination events per genome. Due to the large number of events, they limited analysis to LT2 acquiring sequence from outside subsp enterica and found 347 kb of acquired sequence.
  • They did individual gene trees and then a consensus tree – the presence of highly incongruent trees indicated recombination.
  • Much of the results is dedicated to gene content differences, which I won’t go into here.

Conclusions

  • There were phylogenetically distinct but functionally similar gene clusters e.g. T6SS, T3SS, fimbrial clusters, iron acquisition systems, cytolethal toxins and anerobic respiratory reducatases.
  • Fucntional characterisation of the genes that are unique to subsp enterica is the next step, many of these are poorly characterised or hypothetical. This may result in insight intohow subsp enterica adapted to warm blooded hosts.
  • Used three methods to identify a congruent topology of Salmonella enterica subspecies.
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