Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Paul M. Berube; Steven J. Biller; Thomas Hackl; Shane L. Hogle; Brandon M. Satinsky; Jamie W. Becker; Rogier Braakman; Sara B. Collins; Libusha Kelly; Jessie Berta-Thompson; Allison Coe; Kristin Bergauer; Heather A. Bouman; Thomas J. Browning; Daniele De Corte; Christel Hassler; Yotam Hulata; Jeremy E. Jacquot; Elizabeth W. Maas; Thomas Reinthaler; Eva Sintes; Taichi Yokokawa; Debbie Lindell; Ramunas Stepanauskas; Sallie W. Chisholm

doi:10.1038/sdata.2018.154

Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Paul M. Berube, Steven J. Biller, Thomas Hackl, Shane L. Hogle, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas ReinthalerEva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm

Systems & Computational Biology

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

50 Scopus citations

Abstract

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

Original language	English (US)
Article number	180154
Journal	Scientific Data
Volume	5
DOIs	https://doi.org/10.1038/sdata.2018.154
State	Published - 2018

ASJC Scopus subject areas

Statistics and Probability
Information Systems
Education
Computer Science Applications
Statistics, Probability and Uncertainty
Library and Information Sciences

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/sdata.2018.154

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Berube, P. M., Biller, S. J., Hackl, T., Hogle, S. L., Satinsky, B. M., Becker, J. W., Braakman, R., Collins, S. B., Kelly, L., Berta-Thompson, J., Coe, A., Bergauer, K., Bouman, H. A., Browning, T. J., De Corte, D., Hassler, C., Hulata, Y., Jacquot, J. E., Maas, E. W., ... Chisholm, S. W. (2018). Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Scientific Data, 5, Article 180154. https://doi.org/10.1038/sdata.2018.154

Berube, PM, Biller, SJ, Hackl, T, Hogle, SL, Satinsky, BM, Becker, JW, Braakman, R, Collins, SB, Kelly, L, Berta-Thompson, J, Coe, A, Bergauer, K, Bouman, HA, Browning, TJ, De Corte, D, Hassler, C, Hulata, Y, Jacquot, JE, Maas, EW, Reinthaler, T, Sintes, E, Yokokawa, T, Lindell, D, Stepanauskas, R & Chisholm, SW 2018, 'Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments', Scientific Data, vol. 5, 180154. https://doi.org/10.1038/sdata.2018.154

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title = "Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments",

abstract = "Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.",

author = "Berube, {Paul M.} and Biller, {Steven J.} and Thomas Hackl and Hogle, {Shane L.} and Satinsky, {Brandon M.} and Becker, {Jamie W.} and Rogier Braakman and Collins, {Sara B.} and Libusha Kelly and Jessie Berta-Thompson and Allison Coe and Kristin Bergauer and Bouman, {Heather A.} and Browning, {Thomas J.} and {De Corte}, Daniele and Christel Hassler and Yotam Hulata and Jacquot, {Jeremy E.} and Maas, {Elizabeth W.} and Thomas Reinthaler and Eva Sintes and Taichi Yokokawa and Debbie Lindell and Ramunas Stepanauskas and Chisholm, {Sallie W.}",

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year = "2018",

doi = "10.1038/sdata.2018.154",

language = "English (US)",

volume = "5",

journal = "Scientific Data",

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AU - Berube, Paul M.

AU - Biller, Steven J.

AU - Hackl, Thomas

AU - Hogle, Shane L.

AU - Satinsky, Brandon M.

AU - Becker, Jamie W.

AU - Braakman, Rogier

AU - Collins, Sara B.

AU - Kelly, Libusha

AU - Berta-Thompson, Jessie

AU - Coe, Allison

AU - Bergauer, Kristin

AU - Bouman, Heather A.

AU - Browning, Thomas J.

AU - De Corte, Daniele

AU - Hassler, Christel

AU - Hulata, Yotam

AU - Jacquot, Jeremy E.

AU - Maas, Elizabeth W.

AU - Reinthaler, Thomas

AU - Sintes, Eva

AU - Yokokawa, Taichi

AU - Lindell, Debbie

AU - Stepanauskas, Ramunas

AU - Chisholm, Sallie W.

PY - 2018

Y1 - 2018

N2 - Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

AB - Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

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Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Abstract

ASJC Scopus subject areas

UN SDGs

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