Environmental Genome Shotgun Sequencing of the Sargasso Sea

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

doi:10.1126/science.1093857

Environmental Genome Shotgun Sequencing of the Sargasso Sea

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3380 Citations (Scopus)

Abstract

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-tike photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

Original language	English
Pages (from-to)	66-74
Number of pages	9
Journal	Science
Volume	304
Issue number	5667
DOIs	https://doi.org/10.1126/science.1093857
Publication status	Published - 2 Apr 2004
Externally published	Yes

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Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., ... Smith, H. O. (2004). Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science, 304(5667), 66-74. https://doi.org/10.1126/science.1093857

@article{edc67a9f0f2644f69331697de7d44876,

title = "Environmental Genome Shotgun Sequencing of the Sargasso Sea",

abstract = "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-tike photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.",

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

year = "2004",

month = apr,

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doi = "10.1126/science.1093857",

language = "English",

volume = "304",

pages = "66--74",

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Venter, JC, Remington, K, Heidelberg, JF, Halpern, AL, Rusch, D, Eisen, JA, Wu, D, Paulsen, I, Nelson, KE, Nelson, W, Fouts, DE, Levy, S, Knap, AH, Lomas, MW, Nealson, K, White, O, Peterson, J, Hoffman, J, Parsons, R, Baden-Tillson, H, Pfannkoch, C, Rogers, YH & Smith, HO 2004, 'Environmental Genome Shotgun Sequencing of the Sargasso Sea', Science, vol. 304, no. 5667, pp. 66-74. https://doi.org/10.1126/science.1093857

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T1 - Environmental Genome Shotgun Sequencing of the Sargasso Sea

AU - Venter, J. Craig

AU - Remington, Karin

AU - Heidelberg, John F.

AU - Halpern, Aaron L.

AU - Rusch, Doug

AU - Eisen, Jonathan A.

AU - Wu, Dongying

AU - Paulsen, Ian

AU - Nelson, Karen E.

AU - Nelson, William

AU - Fouts, Derrick E.

AU - Levy, Samuel

AU - Knap, Anthony H.

AU - Lomas, Michael W.

AU - Nealson, Ken

AU - White, Owen

AU - Peterson, Jeremy

AU - Hoffman, Jeff

AU - Parsons, Rachel

AU - Baden-Tillson, Holly

AU - Pfannkoch, Cynthia

AU - Rogers, Yu Hui

AU - Smith, Hamilton O.

PY - 2004/4/2

Y1 - 2004/4/2

N2 - 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-tike photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

AB - 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-tike photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

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SN - 0036-8075

VL - 304

SP - 66

EP - 74

JO - Science

JF - Science

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Environmental Genome Shotgun Sequencing of the Sargasso Sea

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