The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

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Keeling, Patrick J.
Burki, Fabien
Wilcox, Heather M.
Allam, Bassem
Allen, Eric E.
Amaral-Zettler, Linda A.
Armbrust, E. Virginia
Archibald, John M.
Bharti, Arvind K.
Bell, Callum J.
Beszteri, Bank
Bidle, Kay D.
Cameron, Connor T.
Campbell, Lisa
Caron, David A.
Cattolico, Rose Ann
Collier, Jackie L.
Coyne, Kathryn J.
Davy, Simon K.
Deschamps, Phillipe
Dyhrman, Sonya T.
Edvardsen, Bente
Gates, Ruth D.
Gobler, Christopher J.
Greenwood, Spencer J.
Guida, Stephanie M.
Jacobi, Jennifer L.
Jakobsen, Kjetill S.
James, Erick R.
Jenkins, Bethany D.
John, Uwe
Johnson, Matthew D.
Juhl, Andrew R.
Kamp, Anja
Katz, Laura A.
Kiene, Ronald P.
Kudryavtsev, Alexander N.
Leander, Brian S.
Lin, Senjie
Lovejoy, Connie
Lynn, Denis
Marchetti, Adrian
McManus, George
Nedelcu, Aurora M.
Menden-Deuer, Susanne
Miceli, Cristina
Mock, Thomas
Montresor, Marina
Moran, Mary Ann
Murray, Shauna A.
Nadathur, Govind
Nagai, Satoshi
Ngam, Peter B.
Palenik, Brian
Pawlowski, Jan
Petroni, Giulio
Piganeau, Gwenael
Posewitz, Matthew C.
Rengefors, Karin
Romano, Giovanna
Rumpho, Mary E.
Rynearson, Tatiana A.
Schilling, Kelly B.
Schroeder, Declan C.
Simpson, Alastair G. B.
Slamovits, Claudio H.
Smith, David R.
Smith, G. Jason
Smith, Sarah R.
Sosik, Heidi M.
Stief, Peter
Theriot, Edward
Twary, Scott N.
Umale, Pooja E.
Vaulot, Daniel
Wawrik, Boris
Wheeler, Glen L.
Wilson, William H.
Xu, Yan
Zingone, Adriana
Worden, Alexandra Z.
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Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
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PLoS Biology 12 (2014): e1001889
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