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Genetic flux over time in the Salmonella lineage.

Vernikos GS, Thomson NR, Parkhill J - Genome Biol. (2007)

Bottom Line: However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity.Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies.The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

ABSTRACT

Background: DNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene transfer. Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration).

Results: From a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.

Conclusion: The results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.

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G+C content over the three codon positions. Chi-square values of G+C content over the three codon positions for genes assigned to lineages of increasing depth in the reference tree topology. Chi-square values were calculated using the expected G+C codon-position values derived from the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). At the right-bottom side of the figure, the correlation between genomic G+C content and G+C content at the three codon positions based on the data provided by Muto and Osawa [50] is provided. Genes that are still under the amelioration process are expected to deviate from those expected values. The expected G+C content for each codon position in the Salmonella lineage is highlighted in red.
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Figure 6: G+C content over the three codon positions. Chi-square values of G+C content over the three codon positions for genes assigned to lineages of increasing depth in the reference tree topology. Chi-square values were calculated using the expected G+C codon-position values derived from the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). At the right-bottom side of the figure, the correlation between genomic G+C content and G+C content at the three codon positions based on the data provided by Muto and Osawa [50] is provided. Genes that are still under the amelioration process are expected to deviate from those expected values. The expected G+C content for each codon position in the Salmonella lineage is highlighted in red.

Mentions: PHA genes assigned to branch 4[TS] on the Typhi-Paratyphi A lineage show a very strong compositional deviation, indicated both by their very low G+C content of 43.3% (gene average: 53.2%) and the IVOMs score of 0.093 (genome average: 0.059). Furthermore, the codon-position specific G+C content of genes assigned to branch 4[TS] deviate strongly (GC1 = 49%, GC2 = 37%, GC3 = 43%; Figure 6) from the expected values (GC1 = 59%, GC2 = 41%, GC3 = 56%, respectively) based on the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). The G+C content of the second codon position is generally very constrained to similar values across species [3], given that most possible nucleotide substitutions would result in a change in the encoded amino acid residue (non-synonymous substitutions). Interestingly, genes assigned to branch 4[TS] in the Typhi-Paratyphi A lineage also show a significant deviation in this compositionally well-conserved codon position, possibly suggesting a distantly related donor genome.


Genetic flux over time in the Salmonella lineage.

Vernikos GS, Thomson NR, Parkhill J - Genome Biol. (2007)

G+C content over the three codon positions. Chi-square values of G+C content over the three codon positions for genes assigned to lineages of increasing depth in the reference tree topology. Chi-square values were calculated using the expected G+C codon-position values derived from the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). At the right-bottom side of the figure, the correlation between genomic G+C content and G+C content at the three codon positions based on the data provided by Muto and Osawa [50] is provided. Genes that are still under the amelioration process are expected to deviate from those expected values. The expected G+C content for each codon position in the Salmonella lineage is highlighted in red.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394748&req=5

Figure 6: G+C content over the three codon positions. Chi-square values of G+C content over the three codon positions for genes assigned to lineages of increasing depth in the reference tree topology. Chi-square values were calculated using the expected G+C codon-position values derived from the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). At the right-bottom side of the figure, the correlation between genomic G+C content and G+C content at the three codon positions based on the data provided by Muto and Osawa [50] is provided. Genes that are still under the amelioration process are expected to deviate from those expected values. The expected G+C content for each codon position in the Salmonella lineage is highlighted in red.
Mentions: PHA genes assigned to branch 4[TS] on the Typhi-Paratyphi A lineage show a very strong compositional deviation, indicated both by their very low G+C content of 43.3% (gene average: 53.2%) and the IVOMs score of 0.093 (genome average: 0.059). Furthermore, the codon-position specific G+C content of genes assigned to branch 4[TS] deviate strongly (GC1 = 49%, GC2 = 37%, GC3 = 43%; Figure 6) from the expected values (GC1 = 59%, GC2 = 41%, GC3 = 56%, respectively) based on the three linear equations provided by Lawrence and Ochman [3] (see equations 13, 14 and 15 therein). The G+C content of the second codon position is generally very constrained to similar values across species [3], given that most possible nucleotide substitutions would result in a change in the encoded amino acid residue (non-synonymous substitutions). Interestingly, genes assigned to branch 4[TS] in the Typhi-Paratyphi A lineage also show a significant deviation in this compositionally well-conserved codon position, possibly suggesting a distantly related donor genome.

Bottom Line: However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity.Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies.The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

ABSTRACT

Background: DNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene transfer. Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration).

Results: From a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.

Conclusion: The results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.

Show MeSH
Related in: MedlinePlus