Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

[1]  P. Bork,et al.  A global ocean atlas of eukaryotic genes , 2018, Nature Communications.

[2]  O. Jaillon,et al.  Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells , 2017, Scientific Reports.

[3]  E. Pelletier,et al.  Survey of the green picoalga Bathycoccus genomes in the global ocean , 2016, Scientific Reports.

[4]  D. Moreira,et al.  A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts). , 2016, Molecular biology and evolution.

[5]  Luis Pedro Coelho,et al.  Plankton networks driving carbon export in the oligotrophic ocean , 2015, Nature.

[6]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[7]  P. Bork,et al.  Eukaryotic plankton diversity in the sunlit ocean , 2015, Science.

[8]  Peer Bork,et al.  Determinants of community structure in the global plankton interactome , 2015, Science.

[9]  Peer Bork,et al.  Open science resources for the discovery and analysis of Tara Oceans data , 2015, Scientific Data.

[10]  S. Giovannoni,et al.  Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes , 2015, Science.

[11]  Participants Tara Oceans Expedition.  Methodological context of all samples from the Tara Oceans Expedition (2009-2013) , 2015 .

[12]  Michael Y. Galperin,et al.  Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..

[13]  Alexander Schliep,et al.  Single cell genome analysis of an uncultured heterotrophic stramenopile , 2014, Scientific Reports.

[14]  T. R. Anderson,et al.  Reconciliation of the carbon budget in the ocean’s twilight zone , 2014, Nature.

[15]  Pedro M. Coutinho,et al.  The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..

[16]  S. Audic,et al.  Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles , 2013, The ISME Journal.

[17]  T. Cavalier-smith,et al.  Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes. , 2013, European journal of protistology.

[18]  Niels W. Hanson,et al.  Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean , 2013, Proceedings of the National Academy of Sciences.

[19]  David W. Cheung,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[20]  R. Lasken.  Genomic sequencing of uncultured microorganisms from single cells , 2012, Nature Reviews Microbiology.

[21]  Matthew Z. DeMaere,et al.  Global biogeography of SAR11 marine bacteria , 2012, Molecular systems biology.

[22]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[23]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[24]  David M Schruth,et al.  Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability , 2012, Proceedings of the National Academy of Sciences.

[25]  P. Bork,et al.  A Holistic Approach to Marine Eco-Systems Biology , 2011, PLoS biology.

[26]  P. Pevzner,et al.  Efficient de novo assembly of single-cell bacterial genomes from short-read data sets , 2011, Nature Biotechnology.

[27]  R. Stepanauskas,et al.  Unveiling in situ interactions between marine protists and bacteria through single cell sequencing , 2011, The ISME Journal.

[28]  J. del Campo,et al.  Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys. , 2011, Protist.

[29]  R. Stepanauskas,et al.  Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists , 2011, Science.

[30]  R. Stepanauskas,et al.  Capturing diversity of marine heterotrophic protists: one cell at a time , 2011, The ISME Journal.

[31]  C. Slamovits,et al.  Correction: Corrigendum: A bacterial proteorhodopsin proton pump in marine eukaryotes , 2011, Nature Communications.

[32]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[33]  D. Moreira,et al.  Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3. , 2010, Environmental microbiology.

[34]  S. Chisholm,et al.  Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. , 2009, Environmental microbiology.

[35]  F. Not,et al.  Grazing rates and functional diversity of uncultured heterotrophic flagellates , 2009, The ISME Journal.

[36]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[37]  M. Meselson,et al.  Massive Horizontal Gene Transfer in Bdelloid Rotifers , 2008, Science.

[38]  Debashish Bhattacharya,et al.  Phylogeny of nuclear-encoded plastid-targeted proteins supports an early divergence of glaucophytes within Plantae. , 2007, Molecular biology and evolution.

[39]  F. Azam,et al.  Microbial structuring of marine ecosystems , 2007, Nature Reviews Microbiology.

[40]  C. Pedrós-Alió,et al.  Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles , 2004, Applied and Environmental Microbiology.

[41]  E. Koonin,et al.  Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. , 2000, Science.

[42]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[43]  P. Bork,et al.  Descriptor : Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition , 2017 .

[44]  I. Boothby.  One Cell at a Time , 2015, Cell.

[45]  H. Lester,et al.  Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean , 2011 .