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Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.

Kanhere A, Vingron M - BMC Evol. Biol. (2009)

Bottom Line: One successful approach to the detection of HGT events is due to Novichkov et al. (J.Genes transferred between the archaea and bacteria are mostly metabolic genes.On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. a.kanhere@ucl.ac.uk

ABSTRACT

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.

Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.

Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

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Schematic diagram of changes in protein distances with HGT. (A) In a protein family where no horizontal transfer of gene has occurred, the protein tree will exactly follow species tree. In such a case, plotting genomic distances vs. protein distances will show a perfect correlation. (B) On the other hand, if a gene is horizontally transferred, e.g., from species SA to species SB, the protein tree will not resemble the species tree. In this case, some protein distances (like BC) will appear to be greater and some other protein distances (like AB) will appear to be smaller than the corresponding genomic distances. These outlying points (BC, AB) will result in disturbance in correlation and can be detected with Cook's distance.
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Figure 1: Schematic diagram of changes in protein distances with HGT. (A) In a protein family where no horizontal transfer of gene has occurred, the protein tree will exactly follow species tree. In such a case, plotting genomic distances vs. protein distances will show a perfect correlation. (B) On the other hand, if a gene is horizontally transferred, e.g., from species SA to species SB, the protein tree will not resemble the species tree. In this case, some protein distances (like BC) will appear to be greater and some other protein distances (like AB) will appear to be smaller than the corresponding genomic distances. These outlying points (BC, AB) will result in disturbance in correlation and can be detected with Cook's distance.

Mentions: Novichkov et al. proposed a robust approach for detecting HGTs which involves neither building phylogenetic trees nor compositional analysis [13]. This approach is based on comparing evolutionary distances within a set of orthologs to corresponding intergenomic distances (Figure 1). In the absence of HGT and under uniform evolutionary rates, one expects that evolutionary distances between orthologs and corresponding intergenomic distances display a linear relationship (Figure 1A). A gene transfer between a donor species and an acceptor species, however, will result in outliers (Fig. 1B). Novichkov et al. used multiple statistical tests to rank genes according to their probability to have been horizontally transferred. They applied this method to selected genomes and to selected groups of orthologous proteins (Clusters of Orthologous Groups of proteins, COGs), which share same function [14]. This approach was designed to detect xenologous gene displacement (XGD), in which a gene is displaced by an ortholog from different lineage.


Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.

Kanhere A, Vingron M - BMC Evol. Biol. (2009)

Schematic diagram of changes in protein distances with HGT. (A) In a protein family where no horizontal transfer of gene has occurred, the protein tree will exactly follow species tree. In such a case, plotting genomic distances vs. protein distances will show a perfect correlation. (B) On the other hand, if a gene is horizontally transferred, e.g., from species SA to species SB, the protein tree will not resemble the species tree. In this case, some protein distances (like BC) will appear to be greater and some other protein distances (like AB) will appear to be smaller than the corresponding genomic distances. These outlying points (BC, AB) will result in disturbance in correlation and can be detected with Cook's distance.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651853&req=5

Figure 1: Schematic diagram of changes in protein distances with HGT. (A) In a protein family where no horizontal transfer of gene has occurred, the protein tree will exactly follow species tree. In such a case, plotting genomic distances vs. protein distances will show a perfect correlation. (B) On the other hand, if a gene is horizontally transferred, e.g., from species SA to species SB, the protein tree will not resemble the species tree. In this case, some protein distances (like BC) will appear to be greater and some other protein distances (like AB) will appear to be smaller than the corresponding genomic distances. These outlying points (BC, AB) will result in disturbance in correlation and can be detected with Cook's distance.
Mentions: Novichkov et al. proposed a robust approach for detecting HGTs which involves neither building phylogenetic trees nor compositional analysis [13]. This approach is based on comparing evolutionary distances within a set of orthologs to corresponding intergenomic distances (Figure 1). In the absence of HGT and under uniform evolutionary rates, one expects that evolutionary distances between orthologs and corresponding intergenomic distances display a linear relationship (Figure 1A). A gene transfer between a donor species and an acceptor species, however, will result in outliers (Fig. 1B). Novichkov et al. used multiple statistical tests to rank genes according to their probability to have been horizontally transferred. They applied this method to selected genomes and to selected groups of orthologous proteins (Clusters of Orthologous Groups of proteins, COGs), which share same function [14]. This approach was designed to detect xenologous gene displacement (XGD), in which a gene is displaced by an ortholog from different lineage.

Bottom Line: One successful approach to the detection of HGT events is due to Novichkov et al. (J.Genes transferred between the archaea and bacteria are mostly metabolic genes.On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. a.kanhere@ucl.ac.uk

ABSTRACT

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.

Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.

Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

Show MeSH
Related in: MedlinePlus