Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequen...

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Autores principales:	Jenna Morgan Lang, Aaron E Darling, Jonathan A Eisen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/512400c595964b93a45603cd8e1dcb50
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spelling	oai:doaj.org-article:512400c595964b93a45603cd8e1dcb502021-11-18T07:47:49ZPhylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.1932-620310.1371/journal.pone.0062510https://doaj.org/article/512400c595964b93a45603cd8e1dcb502013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23638103/?tool=EBIhttps://doaj.org/toc/1932-6203Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.Jenna Morgan LangAaron E DarlingJonathan A EisenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e62510 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jenna Morgan Lang Aaron E Darling Jonathan A Eisen Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
description	Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.
format	article
author	Jenna Morgan Lang Aaron E Darling Jonathan A Eisen
author_facet	Jenna Morgan Lang Aaron E Darling Jonathan A Eisen
author_sort	Jenna Morgan Lang
title	Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
title_short	Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
title_full	Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
title_fullStr	Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
title_full_unstemmed	Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
title_sort	phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/512400c595964b93a45603cd8e1dcb50
work_keys_str_mv	AT jennamorganlang phylogenyofbacterialandarchaealgenomesusingconservedgenessupertreesandsupermatrices AT aaronedarling phylogenyofbacterialandarchaealgenomesusingconservedgenessupertreesandsupermatrices AT jonathanaeisen phylogenyofbacterialandarchaealgenomesusingconservedgenessupertreesandsupermatrices
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Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

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