Literature DB >> 25977791

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus.

Steven J Biller1, Paul M Berube1, Jessie W Berta-Thompson2, Libusha Kelly1, Sara E Roggensack1, Lana Awad1, Kathryn H Roache-Johnson3, Huiming Ding4, Stephen J Giovannoni5, Gabrielle Rocap6, Lisa R Moore3, Sallie W Chisholm4.   

Abstract

The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity-both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.

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Year:  2014        PMID: 25977791      PMCID: PMC4421930          DOI: 10.1038/sdata.2014.34

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  49 in total

1.  Microbial community gene expression in ocean surface waters.

Authors:  Jorge Frias-Lopez; Yanmei Shi; Gene W Tyson; Maureen L Coleman; Stephan C Schuster; Sallie W Chisholm; Edward F Delong
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-03       Impact factor: 11.205

2.  Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent.

Authors:  Libusha Kelly; Huiming Ding; Katherine H Huang; Marcia S Osburne; Sallie W Chisholm
Journal:  ISME J       Date:  2013-05-09       Impact factor: 10.302

3.  Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes.

Authors:  L R Moore; G Rocap; S W Chisholm
Journal:  Nature       Date:  1998-06-04       Impact factor: 49.962

4.  Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria).

Authors:  E Urbach; D J Scanlan; D L Distel; J B Waterbury; S W Chisholm
Journal:  J Mol Evol       Date:  1998-02       Impact factor: 2.395

5.  Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.

Authors:  Nadav Kashtan; Sara E Roggensack; Sébastien Rodrigue; Jessie W Thompson; Steven J Biller; Allison Coe; Huiming Ding; Pekka Marttinen; Rex R Malmstrom; Roman Stocker; Michael J Follows; Ramunas Stepanauskas; Sallie W Chisholm
Journal:  Science       Date:  2014-04-25       Impact factor: 47.728

6.  Accelerated evolution associated with genome reduction in a free-living prokaryote.

Authors:  Alexis Dufresne; Laurence Garczarek; Frédéric Partensky
Journal:  Genome Biol       Date:  2005-01-14       Impact factor: 13.583

7.  ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage.

Authors:  Libusha Kelly; Katherine H Huang; Huiming Ding; Sallie W Chisholm
Journal:  Nucleic Acids Res       Date:  2011-11-18       Impact factor: 16.971

8.  Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Authors:  Sergey Koren; Michael C Schatz; Brian P Walenz; Jeffrey Martin; Jason T Howard; Ganeshkumar Ganapathy; Zhong Wang; David A Rasko; W Richard McCombie; Erich D Jarvis
Journal:  Nat Biotechnol       Date:  2012-07-01       Impact factor: 54.908

9.  The RAST Server: rapid annotations using subsystems technology.

Authors:  Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko
Journal:  BMC Genomics       Date:  2008-02-08       Impact factor: 3.969

10.  Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.

Authors:  Gregory C Kettler; Adam C Martiny; Katherine Huang; Jeremy Zucker; Maureen L Coleman; Sebastien Rodrigue; Feng Chen; Alla Lapidus; Steven Ferriera; Justin Johnson; Claudia Steglich; George M Church; Paul Richardson; Sallie W Chisholm
Journal:  PLoS Genet       Date:  2007-12       Impact factor: 5.917

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  41 in total

1.  Global biogeography of Prochlorococcus genome diversity in the surface ocean.

Authors:  Alyssa G Kent; Chris L Dupont; Shibu Yooseph; Adam C Martiny
Journal:  ISME J       Date:  2016-02-02       Impact factor: 10.302

Review 2.  Prochlorococcus: the structure and function of collective diversity.

Authors:  Steven J Biller; Paul M Berube; Debbie Lindell; Sallie W Chisholm
Journal:  Nat Rev Microbiol       Date:  2014-12-01       Impact factor: 60.633

3.  Physiology and evolution of nitrate acquisition in Prochlorococcus.

Authors:  Paul M Berube; Steven J Biller; Alyssa G Kent; Jessie W Berta-Thompson; Sara E Roggensack; Kathryn H Roache-Johnson; Marcia Ackerman; Lisa R Moore; Joshua D Meisel; Daniel Sher; Luke R Thompson; Lisa Campbell; Adam C Martiny; Sallie W Chisholm
Journal:  ISME J       Date:  2014-10-28       Impact factor: 10.302

4.  Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes.

Authors:  Luke R Thompson; Mohamed F Haroon; Ahmed A Shibl; Matt J Cahill; David K Ngugi; Gareth J Williams; James T Morton; Rob Knight; Kelly D Goodwin; Ulrich Stingl
Journal:  Appl Environ Microbiol       Date:  2019-06-17       Impact factor: 4.792

5.  Metabolic evolution and the self-organization of ecosystems.

Authors:  Rogier Braakman; Michael J Follows; Sallie W Chisholm
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-27       Impact factor: 11.205

6.  Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes.

Authors:  Haiwei Luo; Yongjie Huang; Ramunas Stepanauskas; Jijun Tang
Journal:  Nat Microbiol       Date:  2017-06-12       Impact factor: 17.745

7.  Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing.

Authors:  Paula Huber; Francisco M Cornejo-Castillo; Isabel Ferrera; Pablo Sánchez; Ramiro Logares; Sebastián Metz; Vanessa Balagué; Silvia G Acinas; Josep M Gasol; Fernando Unrein
Journal:  Appl Environ Microbiol       Date:  2019-03-22       Impact factor: 4.792

8.  Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria.

Authors:  Gregory K Farrant; Hugo Doré; Francisco M Cornejo-Castillo; Frédéric Partensky; Morgane Ratin; Martin Ostrowski; Frances D Pitt; Patrick Wincker; David J Scanlan; Daniele Iudicone; Silvia G Acinas; Laurence Garczarek
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-02       Impact factor: 11.205

Review 9.  Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Authors:  Mak A Saito; Erin M Bertrand; Megan E Duffy; David A Gaylord; Noelle A Held; William Judson Hervey; Robert L Hettich; Pratik D Jagtap; Michael G Janech; Danie B Kinkade; Dagmar H Leary; Matthew R McIlvin; Eli K Moore; Robert M Morris; Benjamin A Neely; Brook L Nunn; Jaclyn K Saunders; Adam I Shepherd; Nicholas I Symmonds; David A Walsh
Journal:  J Proteome Res       Date:  2019-03-12       Impact factor: 4.466

10.  Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals.

Authors:  Dikla Aharonovich; Daniel Sher
Journal:  ISME J       Date:  2016-04-29       Impact factor: 10.302

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