Cargando…

Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

BACKGROUND: One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the...

Descripción completa

Detalles Bibliográficos
Autores principales: Gao, Lei, Qi, Ji
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839080/
https://www.ncbi.nlm.nih.gov/pubmed/17359548
http://dx.doi.org/10.1186/1471-2148-7-41
_version_ 1782132845588774912
author Gao, Lei
Qi, Ji
author_facet Gao, Lei
Qi, Ji
author_sort Gao, Lei
collection PubMed
description BACKGROUND: One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses. RESULTS: The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families. CONCLUSION: With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.
format Text
id pubmed-1839080
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-18390802007-03-30 Whole genome molecular phylogeny of large dsDNA viruses using composition vector method Gao, Lei Qi, Ji BMC Evol Biol Research Article BACKGROUND: One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses. RESULTS: The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families. CONCLUSION: With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses. BioMed Central 2007-03-15 /pmc/articles/PMC1839080/ /pubmed/17359548 http://dx.doi.org/10.1186/1471-2148-7-41 Text en Copyright © 2007 Gao and Qi; 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
Gao, Lei
Qi, Ji
Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title_full Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title_fullStr Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title_full_unstemmed Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title_short Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
title_sort whole genome molecular phylogeny of large dsdna viruses using composition vector method
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839080/
https://www.ncbi.nlm.nih.gov/pubmed/17359548
http://dx.doi.org/10.1186/1471-2148-7-41
work_keys_str_mv AT gaolei wholegenomemolecularphylogenyoflargedsdnavirusesusingcompositionvectormethod
AT qiji wholegenomemolecularphylogenyoflargedsdnavirusesusingcompositionvectormethod