Cargando…

Modelling prokaryote gene content

The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical ev...

Descripción completa

Detalles Bibliográficos
Autores principales: Spencer, Matthew, Susko, Edward, Roger, Andrew J.
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674660/
https://www.ncbi.nlm.nih.gov/pubmed/19455209
_version_ 1782166660613931008
author Spencer, Matthew
Susko, Edward
Roger, Andrew J.
author_facet Spencer, Matthew
Susko, Edward
Roger, Andrew J.
author_sort Spencer, Matthew
collection PubMed
description The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.
format Text
id pubmed-2674660
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher Libertas Academica
record_format MEDLINE/PubMed
spelling pubmed-26746602009-05-19 Modelling prokaryote gene content Spencer, Matthew Susko, Edward Roger, Andrew J. Evol Bioinform Online Original Research The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model. Libertas Academica 2007-02-05 /pmc/articles/PMC2674660/ /pubmed/19455209 Text en Copyright © 2006 The authors. http://creativecommons.org/licenses/by/3.0 This article is published under the Creative Commons Attribution By licence. For further information go to: http://creativecommons.org/licenses/by/3.0. (http://creativecommons.org/licenses/by/3.0)
spellingShingle Original Research
Spencer, Matthew
Susko, Edward
Roger, Andrew J.
Modelling prokaryote gene content
title Modelling prokaryote gene content
title_full Modelling prokaryote gene content
title_fullStr Modelling prokaryote gene content
title_full_unstemmed Modelling prokaryote gene content
title_short Modelling prokaryote gene content
title_sort modelling prokaryote gene content
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674660/
https://www.ncbi.nlm.nih.gov/pubmed/19455209
work_keys_str_mv AT spencermatthew modellingprokaryotegenecontent
AT suskoedward modellingprokaryotegenecontent
AT rogerandrewj modellingprokaryotegenecontent