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Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori
BACKGROUND: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of e...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2005
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC549213/ https://www.ncbi.nlm.nih.gov/pubmed/15676066 http://dx.doi.org/10.1186/1471-2164-6-9 |
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author | Saunders, Nigel J Boonmee, Prawit Peden, John F Jarvis, Stephen A |
author_facet | Saunders, Nigel J Boonmee, Prawit Peden, John F Jarvis, Stephen A |
author_sort | Saunders, Nigel J |
collection | PubMed |
description | BACKGROUND: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. RESULTS: This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. CONCLUSION: New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. |
format | Text |
id | pubmed-549213 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-5492132005-02-23 Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori Saunders, Nigel J Boonmee, Prawit Peden, John F Jarvis, Stephen A BMC Genomics Research Article BACKGROUND: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. RESULTS: This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. CONCLUSION: New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. BioMed Central 2005-01-27 /pmc/articles/PMC549213/ /pubmed/15676066 http://dx.doi.org/10.1186/1471-2164-6-9 Text en Copyright © 2005 Saunders et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Saunders, Nigel J Boonmee, Prawit Peden, John F Jarvis, Stephen A Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title_full | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title_fullStr | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title_full_unstemmed | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title_short | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
title_sort | inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within helicobacter pylori |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC549213/ https://www.ncbi.nlm.nih.gov/pubmed/15676066 http://dx.doi.org/10.1186/1471-2164-6-9 |
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