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Environmental Genome Shotgun Sequencing of the Sargasso Sea

by Peterson, Jeremy , Remington, Karin , Hoffman, Jeff , Heidelberg, John F. , Rusch, Doug , Venter, J. Craig , Pfannkoch, Cynthia , Paulsen, Ian , Lomas, Michael W. , Nealson, Ken , Halpern, Aaron L. , Fouts, Derrick E. , Nelson, William , Wu, Dongying , Nelson, Karen E. , Eisen, Jonathan A. , White, Owen , Parsons, Rachel , Smith, Hamilton O. , Rogers, Yu-Hui , Levy, Samuel , Baden-Tillson, Holly , Knap, Anthony H.

in Algorithms / Animal, plant and microbial ecology / Archaea / Archaea - genetics / Atlantic Ocean / Bacteria - genetics / Bacteriophages / Bacteriophages - genetics / Biodiversity / Biological and medical sciences / Biological taxonomies / Chemical analysis / Computational Biology / Cyanobacteria - genetics / Cyanobacteria - growth & development / Cyanobacteria - metabolism / Ecosystem / Environment / Environmental conditions / Eukaryotic Cells / Fundamental and applied biological sciences. Psychology / Genes, Archaeal / Genes, Bacterial / Genes, rRNA / Genetic aspects / Genome, Archaeal / Genome, Bacterial / Genomes / Genomics / Libraries / Marine / Marine biology / Microbial ecology / Microorganisms / Molecular Sequence Data / Natural history / Observations / Ocean / Oceans / Photosynthesis / Phylogenetics / Phylogeny / Plasmids / Relative abundance / Research Article / Rhodopsin - genetics / Rhodopsins, Microbial / Scaffolds / Seawater / Seawater - microbiology / Sequence Analysis, DNA / Sequencing / Species / Species diversity / Various environments (extraatmospheric space, air, water) / Water / Water analysis / Water Microbiology

2004

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Environmental Genome Shotgun Sequencing of the Sargasso Sea

2004

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Environmental Genome Shotgun Sequencing of the Sargasso Sea

2004

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Journal Article

Environmental Genome Shotgun Sequencing of the Sargasso Sea

Peterson, Jeremy,

Remington, Karin,

Hoffman, Jeff,

Heidelberg, John F.,

Rusch, Doug,

Venter, J. Craig,

Pfannkoch, Cynthia,

Paulsen, Ian,

Lomas, Michael W.,

Nealson, Ken,

Halpern, Aaron L.,

Fouts, Derrick E.,

Nelson, William,

Wu, Dongying,

Nelson, Karen E.,

Eisen, Jonathan A.,

White, Owen,

Parsons, Rachel,

Smith, Hamilton O.,

Rogers, Yu-Hui,

Levy, Samuel,

Baden-Tillson, Holly,

Knap, Anthony H.

2004

Overview

We have applied \"whole-genome shotgun sequencing\" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

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Publisher

American Association for the Advancement of Science,The American Association for the Advancement of Science

Subject

Algorithms

/ Animal, plant and microbial ecology

/ Archaea

/ Archaea - genetics

/ Atlantic Ocean

/ Bacteria - genetics

/ Bacteriophages