The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorc...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060 http://www.ncbi.nlm.nih.gov/pubmed/17355176 https://doi.org/10.1371/journal.pbio.0050077 |
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ftpubmed:oai:pubmedcentral.nih.gov:1821060 2023-05-15T17:35:06+02:00 The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J. Craig 2007-03 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060 http://www.ncbi.nlm.nih.gov/pubmed/17355176 https://doi.org/10.1371/journal.pbio.0050077 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060 http://www.ncbi.nlm.nih.gov/pubmed/17355176 http://dx.doi.org/10.1371/journal.pbio.0050077 Copyright: © 2007 Rusch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2007 ftpubmed https://doi.org/10.1371/journal.pbio.0050077 2013-08-31T18:42:40Z The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be ... Text North Atlantic Northwest Atlantic PubMed Central (PMC) Pacific PLoS Biology 5 3 e77 |
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Research Article |
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Research Article Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J. Craig The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
topic_facet |
Research Article |
description |
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be ... |
format |
Text |
author |
Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J. Craig |
author_facet |
Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J. Craig |
author_sort |
Rusch, Douglas B |
title |
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
title_short |
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
title_full |
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
title_fullStr |
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
title_full_unstemmed |
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific |
title_sort |
sorcerer ii global ocean sampling expedition: northwest atlantic through eastern tropical pacific |
publisher |
Public Library of Science |
publishDate |
2007 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060 http://www.ncbi.nlm.nih.gov/pubmed/17355176 https://doi.org/10.1371/journal.pbio.0050077 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
North Atlantic Northwest Atlantic |
genre_facet |
North Atlantic Northwest Atlantic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060 http://www.ncbi.nlm.nih.gov/pubmed/17355176 http://dx.doi.org/10.1371/journal.pbio.0050077 |
op_rights |
Copyright: © 2007 Rusch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pbio.0050077 |
container_title |
PLoS Biology |
container_volume |
5 |
container_issue |
3 |
container_start_page |
e77 |
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1766134157103071232 |