Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.

<h4>Background</h4>Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new sourc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Dongying Wu, Martin Wu, Aaron Halpern, Douglas B Rusch, Shibu Yooseph, Marvin Frazier, J Craig Venter, Jonathan A Eisen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f786eb7b30b248bbbef393be4155698b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f786eb7b30b248bbbef393be4155698b
record_format	dspace
spelling	oai:doaj.org-article:f786eb7b30b248bbbef393be4155698b2021-11-18T06:57:09ZStalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.1932-620310.1371/journal.pone.0018011https://doaj.org/article/f786eb7b30b248bbbef393be4155698b2011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21437252/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.<h4>Methodology/principal findings</h4>We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.<h4>Conclusions/significance</h4>Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.Dongying WuMartin WuAaron HalpernDouglas B RuschShibu YoosephMarvin FrazierJ Craig VenterJonathan A EisenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e18011 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dongying Wu Martin Wu Aaron Halpern Douglas B Rusch Shibu Yooseph Marvin Frazier J Craig Venter Jonathan A Eisen Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
description	<h4>Background</h4>Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.<h4>Methodology/principal findings</h4>We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.<h4>Conclusions/significance</h4>Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.
format	article
author	Dongying Wu Martin Wu Aaron Halpern Douglas B Rusch Shibu Yooseph Marvin Frazier J Craig Venter Jonathan A Eisen
author_facet	Dongying Wu Martin Wu Aaron Halpern Douglas B Rusch Shibu Yooseph Marvin Frazier J Craig Venter Jonathan A Eisen
author_sort	Dongying Wu
title	Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
title_short	Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
title_full	Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
title_fullStr	Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
title_full_unstemmed	Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
title_sort	stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/f786eb7b30b248bbbef393be4155698b
work_keys_str_mv	AT dongyingwu stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT martinwu stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT aaronhalpern stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT douglasbrusch stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT shibuyooseph stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT marvinfrazier stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT jcraigventer stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees AT jonathanaeisen stalkingthefourthdomaininmetagenomicdatasearchingfordiscoveringandinterpretingnoveldeepbranchesinmarkergenephylogenetictrees
_version_	1718424206076542976

Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.

Ejemplares similares