title: Probing the evolution, ecology and physiology of marine protists using transcriptomics.
abstract: Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic life. This information is providing insights into the adaptations and interactions between protists and other microorganisms and macroorganisms, but many of the genes sequenced show no similarity to sequences currently available in public databases. A better understanding of these newly discovered genes will lead to a deeper appreciation of the functional diversity and metabolic processes in the ocean. In this Review, we summarize recent developments in our understanding of the ecology, physiology and evolution of protists, derived from transcriptomic studies of cultured strains and natural communities, and discuss how these novel large-scale genetic datasets will be used in the future.
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California 90089, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Caron
authors.affiliation: Department of Population Health and Reproduction, School of Veterinary Medicine, 1 Shields Avenue, University of California Davis, Davis, California 95616, USA.
authors.forename: Harriet
authors.initials: H
authors.lastname: Alexander
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, San Diego, California 92037, USA.|Scripps Institution of Oceanography, Integrative Oceanography Division, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, California 92093, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia B3H 4R2, Canada.|Canadian Institute for Advanced Research, 180 Dundas Street W, Toronto, Ontario M5G 1Z8, Canada.
authors.forename: John M
authors.initials: JM
authors.lastname: Archibald
authors.affiliation: School of Oceanography, University of Washington, 1503 NE Boat Street, Seattle, Washington 98195, USA.
authors.forename: E Virginia
authors.initials: EV
authors.lastname: Armbrust
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Bachy
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, New Mexico 87505, USA.
authors.forename: Callum J
authors.initials: CJ
authors.lastname: Bell
authors.affiliation: Syngenta Biotechnology, 629 Davis Drive, Research Triangle Park, North Carolina 27709, USA.
authors.forename: Arvind
authors.initials: A
authors.lastname: Bharti
authors.affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, New York 10964, USA.
authors.forename: Sonya T
authors.initials: ST
authors.lastname: Dyhrman
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, New Mexico 87505, USA.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Guida
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California 90089, USA.
authors.forename: Karla B
authors.initials: KB
authors.lastname: Heidelberg
authors.affiliation: Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California 94304, USA.
authors.forename: Jonathan Z
authors.initials: JZ
authors.lastname: Kaye
authors.affiliation: Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California 94304, USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Metzner
authors.affiliation: Scripps Institution of Oceanography, Integrative Oceanography Division, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, California 92093, USA.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Smith
authors.affiliation: Canadian Institute for Advanced Research, 180 Dundas Street W, Toronto, Ontario M5G 1Z8, Canada.|Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA.
authors.forename: Alexandra Z
authors.initials: AZ
authors.lastname: Worden
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics / Q000502:physiology*; D005075:Biological Evolution; D017753:Ecosystem; D004734:Energy Metabolism / Q000502:physiology*; D056890:Eukaryota / Q000235:genetics / Q000502:physiology*; D059467:Transcriptome / Q000235:genetics*