Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.

Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, parti...

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Autores principales:	Vera Tai, Art F Y Poon, Ian T Paulsen, Brian Palenik
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1839635796f34c2c9ba0654e283b4987
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spelling	oai:doaj.org-article:1839635796f34c2c9ba0654e283b49872021-11-04T06:08:56ZSelection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.1932-620310.1371/journal.pone.0024249https://doaj.org/article/1839635796f34c2c9ba0654e283b49872011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21931665/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, particularly of short, unlinked sequences. A custom analytical pipeline was developed to calculate dN/dS ratios, a common metric to evaluate the role of selection in the evolution of a gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine Synechococcus, the dominant cyanobacteria in coastal environments. The large majority of genes (98%) have evolved under purifying selection (dN/dS<1). The metagenome sequence coverage of the reference genomes was not uniform and genes that were highly represented in the environment (i.e. high read coverage) tended to be more evolutionarily conserved. Of the genes that may have evolved under positive selection (dN/dS>1), 77 out of 83 (93%) were hypothetical. Notable among annotated genes, ribosomal protein L35 appears to be under positive selection in one Synechococcus population. Other annotated genes, in particular a possible porin, a large-conductance mechanosensitive channel, an ATP binding component of an ABC transporter, and a homologue of a pilus retraction protein had regions of the gene with elevated dN/dS. With the increasing use of next-generation sequencing in metagenomic investigations of microbial diversity and ecology, analytical methods need to accommodate the peculiarities of these data streams. By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer.Vera TaiArt F Y PoonIan T PaulsenBrian PalenikPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e24249 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vera Tai Art F Y Poon Ian T Paulsen Brian Palenik Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
description	Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, particularly of short, unlinked sequences. A custom analytical pipeline was developed to calculate dN/dS ratios, a common metric to evaluate the role of selection in the evolution of a gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine Synechococcus, the dominant cyanobacteria in coastal environments. The large majority of genes (98%) have evolved under purifying selection (dN/dS<1). The metagenome sequence coverage of the reference genomes was not uniform and genes that were highly represented in the environment (i.e. high read coverage) tended to be more evolutionarily conserved. Of the genes that may have evolved under positive selection (dN/dS>1), 77 out of 83 (93%) were hypothetical. Notable among annotated genes, ribosomal protein L35 appears to be under positive selection in one Synechococcus population. Other annotated genes, in particular a possible porin, a large-conductance mechanosensitive channel, an ATP binding component of an ABC transporter, and a homologue of a pilus retraction protein had regions of the gene with elevated dN/dS. With the increasing use of next-generation sequencing in metagenomic investigations of microbial diversity and ecology, analytical methods need to accommodate the peculiarities of these data streams. By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer.
format	article
author	Vera Tai Art F Y Poon Ian T Paulsen Brian Palenik
author_facet	Vera Tai Art F Y Poon Ian T Paulsen Brian Palenik
author_sort	Vera Tai
title	Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
title_short	Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
title_full	Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
title_fullStr	Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
title_full_unstemmed	Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
title_sort	selection in coastal synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/1839635796f34c2c9ba0654e283b4987
work_keys_str_mv	AT veratai selectionincoastalsynechococcuscyanobacteriapopulationsevaluatedfromenvironmentalmetagenomes AT artfypoon selectionincoastalsynechococcuscyanobacteriapopulationsevaluatedfromenvironmentalmetagenomes AT iantpaulsen selectionincoastalsynechococcuscyanobacteriapopulationsevaluatedfromenvironmentalmetagenomes AT brianpalenik selectionincoastalsynechococcuscyanobacteriapopulationsevaluatedfromenvironmentalmetagenomes
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Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.

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