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...
Published in: | PLoS Biology |
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2007
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Online Access: | https://hdl.handle.net/10669/87936 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077 https://doi.org/10.1371/journal.pbio.0050077 |
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ftunivcostarica:oai:https://www.kerwa.ucr.ac.cr:10669/87936 2023-05-15T17:35:33+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 Gallardo, Víctor Ariel Tamayo Castillo, Giselle Ferrari, Michael R. Strausberg, Robert L. Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J. Craig 2007-03 application/pdf https://hdl.handle.net/10669/87936 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077 https://doi.org/10.1371/journal.pbio.0050077 eng eng https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077 1545-7885 https://hdl.handle.net/10669/87936 doi:10.1371/journal.pbio.0050077 PLoS Biology, Vol.5(3), pp.0398-0431 EXPLORACIÓN MARINA OCÉANO OCÉANO ATLÁNTICO explora artículo científico 2007 ftunivcostarica https://doi.org/10.1371/journal.pbio.0050077 2022-12-22T00:32:32Z 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 ... Other/Unknown Material North Atlantic Northwest Atlantic Universidad de Costa Rica: Repositorio Kérwá Pacific PLoS Biology 5 3 e77 |
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Universidad de Costa Rica: Repositorio Kérwá |
op_collection_id |
ftunivcostarica |
language |
English |
topic |
EXPLORACIÓN MARINA OCÉANO OCÉANO ATLÁNTICO explora |
spellingShingle |
EXPLORACIÓN MARINA OCÉANO OCÉANO ATLÁNTICO explora 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 Gallardo, Víctor Ariel 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 |
EXPLORACIÓN MARINA OCÉANO OCÉANO ATLÁNTICO explora |
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 |
Other/Unknown Material |
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 Gallardo, Víctor Ariel 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 Gallardo, Víctor Ariel 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 |
publishDate |
2007 |
url |
https://hdl.handle.net/10669/87936 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077 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_source |
PLoS Biology, Vol.5(3), pp.0398-0431 |
op_relation |
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077 1545-7885 https://hdl.handle.net/10669/87936 doi:10.1371/journal.pbio.0050077 |
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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1766134744422023168 |