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Microbial Ecology

, Volume 66, Issue 4, pp 752–762 | Cite as

Genomic Taxonomy of the Genus Prochlorococcus

  • Cristiane C. Thompson
  • Genivaldo G. Z. Silva
  • Nayra M. Vieira
  • Robert Edwards
  • Ana Carolina P. Vicente
  • Fabiano L. Thompson
Microbiology of Aquatic Systems

Abstract

The genus Prochlorococcus is globally abundant and dominates the total phytoplankton biomass and production in the oligotrophic ocean. The single species, Prochlorococcus marinus, comprises six named ecotypes. Our aim was to analyze the taxonomic structure of the genus Prochlorococcus. We analyzed the complete genomes of 13 cultured P. marinus type and reference strains by means of several genomic taxonomy tools (i.e., multilocus sequence analysis, amino acid identity, Karlin genomic signature, and genome to genome distance). In addition, we estimated the diversity of Prochlorococcus species in over 100 marine metagenomes from all the major oceanic provinces. According to our careful taxonomic analysis, the 13 strains corresponded, in fact, to ten different Prochlorococcus species. This analysis establishes a new taxonomic framework for the genus Prochlorococcus. Further, the analysis of the metagenomic data suggests that, in total, there may only be 35 Prochlorococcus species in the world's oceans. We propose that the dearth of species observed in this study is driven by high selective pressures that limit diversification in the global ocean.

Keywords

Amino Acid Identity Prochlorococcus Genomic Signature Taxonomic Structure Multilocus Sequence Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors thank the support of CAPES, FAPERJ, and CNPq.

Supplementary material

248_2013_270_Fig4_ESM.jpg (1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig5_ESM.jpg (1.1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig6_ESM.jpg (1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig7_ESM.jpg (1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig8_ESM.jpg (1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig9_ESM.jpg (1.3 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig10_ESM.jpg (703 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig11_ESM.jpg (713 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig12_ESM.jpg (1 mb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig13_ESM.jpg (424 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig14_ESM.jpg (463 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig15_ESM.jpg (415 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

248_2013_270_Fig16_ESM.jpg (401 kb)
Figs. S1–S13

Fragment recruitment plots of Prochlorococus genomes versus 111 marine metagenomes. X-axis shows the genome size and the Y-axis shows the % identity. (JPEG 1071 kb)

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Table S1 General features of the metagenomic data. (XLSX 93 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Cristiane C. Thompson
    • 1
    • 3
  • Genivaldo G. Z. Silva
    • 2
  • Nayra M. Vieira
    • 3
  • Robert Edwards
    • 2
    • 3
  • Ana Carolina P. Vicente
    • 1
  • Fabiano L. Thompson
    • 3
  1. 1.Laboratory of Molecular Genetics of Microrganisms, Oswaldo Cruz InstituteFIOCRUZRio de JaneiroBrazil
  2. 2.Department of Computer Science and Computational Science Research CenterSan Diego State UniversitySan DiegoUSA
  3. 3.Laboratory of Microbiology, Institute of BiologyFederal University of Rio de Janeiro, UFRJRio de JaneiroBrazil

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