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The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer
With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controve...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2005
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1233574/ https://www.ncbi.nlm.nih.gov/pubmed/16122348 http://dx.doi.org/10.1371/journal.pbio.0030316 |
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author | Ge, Fan Wang, Li-San Kim, Junhyong |
author_facet | Ge, Fan Wang, Li-San Kim, Junhyong |
author_sort | Ge, Fan |
collection | PubMed |
description | With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the “essence of phylogeny” and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches. |
format | Text |
id | pubmed-1233574 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-12335742005-10-13 The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer Ge, Fan Wang, Li-San Kim, Junhyong PLoS Biol Research Article With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the “essence of phylogeny” and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches. Public Library of Science 2005-10 2005-08-30 /pmc/articles/PMC1233574/ /pubmed/16122348 http://dx.doi.org/10.1371/journal.pbio.0030316 Text en Copyright: © 2005 Ge et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Ge, Fan Wang, Li-San Kim, Junhyong The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title | The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title_full | The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title_fullStr | The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title_full_unstemmed | The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title_short | The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer |
title_sort | cobweb of life revealed by genome-scale estimates of horizontal gene transfer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1233574/ https://www.ncbi.nlm.nih.gov/pubmed/16122348 http://dx.doi.org/10.1371/journal.pbio.0030316 |
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