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Levy Karin E, Mirdita M, Söding J. MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. MICROBIOME 2020; 8:48. [PMID: 32245390 PMCID: PMC7126354 DOI: 10.1186/s40168-020-00808-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/14/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. RESULTS MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. CONCLUSION The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.
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Affiliation(s)
- Eli Levy Karin
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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2
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Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis. Sci Rep 2018; 8:8890. [PMID: 29891905 PMCID: PMC5995825 DOI: 10.1038/s41598-018-27172-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/25/2018] [Indexed: 11/17/2022] Open
Abstract
To investigate the differences in the interactions of microbial communities in two regions in Taihu Lake with different nutrient loadings [Meiliang Bay (MLB) and Xukou Bay (XKB)], water samples were collected and both intra- and inter-kingdom microbial community interactions were examined with network analysis. It is demonstrated that all of the bacterioplankton, microeukaryotes and inter-kingdom communities networks in Taihu Lake were non-random. For the networks of bacterioplankton and inter-kingdom community in XKB, higher clustering coefficient and average degree but lower average path length indexes were observed, indicating the nodes in XKB were more clustered and closely connected with plenty edges than those of MLB. The bacterioplankton and inter-kingdom networks were considerably larger and more complex with more module hubs and connectors in XKB compared with those of MLB, whereas the microeukaryotes networks were comparable and had no module hubs or connectors in the two lake zones. The phyla of Acidobacteria, Cyanobacteria and Planctomycetes maintained greater cooperation with other phyla in XKB, rather than competition. The relationships between microbial communities and environmental factors in MLB were weaker. Compared with the microbial community networks of XKB, less modules in networks of MLB were significantly correlated with total phosphorous and total nitrogen.
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Zhao D, Cao X, Huang R, Zeng J, Shen F, Xu H, Wang S, He X, Yu Z. The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake. Appl Microbiol Biotechnol 2017; 101:5913-5923. [PMID: 28523397 DOI: 10.1007/s00253-017-8327-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/02/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022]
Abstract
To investigate the differences in the microbial community composition and assembly process in two lake zones (Meiliang Bay (MLB) and Xukou Bay (XKB) in Taihu Lake, China) with different nutrient loadings, water samples were collected. Both the 16S ribosomal RNA (rRNA) gene for the bacterial community and the 18S rRNA gene for the microeukaryote community were investigated using the Illumina second-generation sequencing platform (2 × 250 paired-end). The results indicated that both the bacterioplankton and microeukaryote community composition derived from the two lake zones were significantly different. Significantly higher operational taxonomic unit (OTU) richness (P < 0.01) and phylogenetic diversity (P < 0.05) were found for the bacterioplankton community of MLB. However, a comparable alpha diversity was found between the microeukaryote communities of MLB and XKB (P > 0.05). Environmental factors significantly affected the community compositions in XKB for both the bacterioplankton and microeukaryotes. However, they did not significantly influence the microbial community composition in MLB, except for a weak correlation between dissolved organic carbon (DOC) and the microeukaryote community. The microbial communities tended to be more phylogenetically clustered than expected by chance in the two lake zones. Moreover, the results of the phylogenetic structure suggest that deterministic processes played overwhelming roles in driving the assembly of both the bacterioplankton and microeukaryote community in XKB.
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Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China. .,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China. .,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Xinyi Cao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Feng Shen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huimin Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Sichen Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiaowei He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China. .,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.
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van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Deerinck TJ, Kuo A, Grigoriev IV, Wong CH, Smith RD, Callister SJ, Wei CL, Schmutz J, Worden AZ. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics 2016; 17:267. [PMID: 27029936 PMCID: PMC4815162 DOI: 10.1186/s12864-016-2585-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/11/2016] [Indexed: 01/26/2023] Open
Abstract
Background Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2585-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marijke J van Baren
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Charles Bachy
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Emily Nahas Reistetter
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Samuel O Purvine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jane Grimwood
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Hang Yu
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.,Now at: Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Thomas J Deerinck
- Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, La Jolla, San Diego, California, 92093, USA
| | - Alan Kuo
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Chee-Hong Wong
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Stephen J Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chia-Lin Wei
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA. .,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.
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5
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Kim EJ, Ma X, Cerutti H. Gene silencing in microalgae: mechanisms and biological roles. BIORESOURCE TECHNOLOGY 2015; 184:23-32. [PMID: 25466994 DOI: 10.1016/j.biortech.2014.10.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 05/18/2023]
Abstract
Microalgae exhibit enormous diversity and can potentially contribute to the production of biofuels and high value compounds. However, for most species, our knowledge of their physiology, metabolism, and gene regulation is fairly limited. In eukaryotes, gene silencing mechanisms play important roles in both the reversible repression of genes that are required only in certain contexts and the suppression of genome invaders such at transposons. The recent sequencing of several algal genomes is providing insights into the complexity of these mechanisms in microalgae. Collectively, glaucophyte, red, and green microalgae contain the machineries involved in repressive histone H3 lysine methylation, DNA cytosine methylation, and RNA interference. However, individual species often only have subsets of these gene silencing mechanisms. Moreover, current evidence suggests that algal silencing systems function in transposon and transgene repression but their role(s) in gene regulation or other cellular processes remains virtually unexplored, hindering rational genetic engineering efforts.
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Affiliation(s)
- Eun-Jeong Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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7
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Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science 2015; 347:1257594. [DOI: 10.1126/science.1257594] [Citation(s) in RCA: 439] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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8
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Reliability of qPCR for quantitative gut content estimation in the circumglobally abundant pelagic tunicate Dolioletta gegenbauri (Tunicata, Thaliacea). FOOD WEBS 2014. [DOI: 10.1016/j.fooweb.2014.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AGB, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 2014; 12:e1001889. [PMID: 24959919 PMCID: PMC4068987 DOI: 10.1371/journal.pbio.1001889] [Citation(s) in RCA: 626] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
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Affiliation(s)
- Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- * E-mail: (PJK); (AZW)
| | - Fabien Burki
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heather M. Wilcox
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Linda A. Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Geological Sciences, Brown University, Providence, Rhode Island, United States of America
| | - E. Virginia Armbrust
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - John M. Archibald
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arvind K. Bharti
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Bank Beszteri
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kay D. Bidle
- Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Connor T. Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Lisa Campbell
- Department of Oceanography, Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - David A. Caron
- Department of Biology, University of Southern California, Los Angeles, California, United States of America
| | - Rose Ann Cattolico
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathryn Coyne
- University of Delaware, School of Marine Science and Policy, College of Earth, Ocean, and Environment, Lewes, Delaware, United States of America
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Phillipe Deschamps
- Unité d'Ecologie, Systematique et Evolution, CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | | | - Ruth D. Gates
- Hawaii Institute of Marine Biology, University of Hawaii, Hawaii, United States of America
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Spencer J. Greenwood
- Department of Biomedical Sciences and AVC Lobster Science Centre, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Stephanie M. Guida
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Jennifer L. Jacobi
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | | | - Erick R. James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bethany Jenkins
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Matthew D. Johnson
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Andrew R. Juhl
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | - Anja Kamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen, Molecular Life Science Research Center, Bremen, Germany
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Ronald Kiene
- University of South Alabama, Dauphin Island Sea Lab, Mobile, Alabama, United States of America
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Brian S. Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, Canada
| | - Denis Lynn
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adrian Marchetti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - George McManus
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Aurora M. Nedelcu
- University of New Brunswick, Department of Biology, Fredericton, New Brusnswick, Canada
| | - Susanne Menden-Deuer
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Shauna Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, Australia
| | - Govind Nadathur
- Department of Marine Sciences, University of Puerto Rico, Mayaguez, Puerto Rico, United States of America
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Kanagawa, Japan
| | - Peter B. Ngam
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Brian Palenik
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Gwenael Piganeau
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, BIOM, Banyuls-sur-Mer, France
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | | | | | - Mary E. Rumpho
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Tatiana Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Kelly B. Schilling
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Declan C. Schroeder
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
| | - Alastair G. B. Simpson
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H. Slamovits
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - G. Jason Smith
- Moss Landing Marine Laboratories, Moss Landing, California, United States of America
| | - Sarah R. Smith
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Heidi M. Sosik
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Peter Stief
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Edward Theriot
- Section of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Scott N. Twary
- Los Alamos National Laboratory, Biosciences, Los Alamos, New Mexico, United States of America
| | - Pooja E. Umale
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Daniel Vaulot
- UMR714, CNRS and UPMC (Paris-06), Station Biologique, Roscoff, France
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Glen L. Wheeler
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
- Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - William H. Wilson
- NCMA, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Yan Xu
- Princeton University, Princeton, New Jersey, United States of America
| | | | - Alexandra Z. Worden
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- * E-mail: (PJK); (AZW)
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10
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Cerutti H, Ma X, Msanne J, Repas T. RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. EUKARYOTIC CELL 2011; 10:1164-72. [PMID: 21803865 PMCID: PMC3187060 DOI: 10.1128/ec.05106-11] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Algae are a large group of aquatic, typically photosynthetic, eukaryotes that include species from very diverse phylogenetic lineages, from those similar to land plants to those related to protist parasites. The recent sequencing of several algal genomes has provided insights into the great complexity of these organisms. Genomic information has also emphasized our lack of knowledge of the functions of many predicted genes, as well as the gene regulatory mechanisms in algae. Core components of the machinery for RNA-mediated silencing show widespread distribution among algal lineages, but they also seem to have been lost entirely from several species with relatively small nuclear genomes. Complex sets of endogenous small RNAs, including candidate microRNAs and small interfering RNAs, have now been identified by high-throughput sequencing in green, red, and brown algae. However, the natural roles of RNA-mediated silencing in algal biology remain poorly understood. Limited evidence suggests that small RNAs may function, in different algae, in defense mechanisms against transposon mobilization, in responses to nutrient deprivation and, possibly, in the regulation of recently evolved developmental processes. From a practical perspective, RNA interference (RNAi) is becoming a promising tool for assessing gene function by sequence-specific knockdown. Transient gene silencing, triggered with exogenously synthesized nucleic acids, and/or stable gene repression, involving genome-integrated transgenes, have been achieved in green algae, diatoms, yellow-green algae, and euglenoids. The development of RNAi technology in conjunction with system level "omics" approaches may provide the tools needed to advance our understanding of algal physiological and metabolic processes.
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Affiliation(s)
- Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, E211 Beadle Center, P.O. Box 880666, Lincoln, NE 68588-0666, USA.
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Stüken A, Orr RJS, Kellmann R, Murray SA, Neilan BA, Jakobsen KS. Discovery of nuclear-encoded genes for the neurotoxin saxitoxin in dinoflagellates. PLoS One 2011; 6:e20096. [PMID: 21625593 PMCID: PMC3097229 DOI: 10.1371/journal.pone.0020096] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 04/12/2011] [Indexed: 11/26/2022] Open
Abstract
Saxitoxin is a potent neurotoxin that occurs in aquatic environments worldwide.
Ingestion of vector species can lead to paralytic shellfish poisoning, a severe
human illness that may lead to paralysis and death. In freshwaters, the toxin is
produced by prokaryotic cyanobacteria; in marine waters, it is associated with
eukaryotic dinoflagellates. However, several studies suggest that saxitoxin is
not produced by dinoflagellates themselves, but by co-cultured bacteria. Here,
we show that genes required for saxitoxin synthesis are encoded in the nuclear
genomes of dinoflagellates. We sequenced >1.2×106 mRNA
transcripts from the two saxitoxin-producing dinoflagellate strains
Alexandrium fundyense CCMP1719 and A.
minutum CCMP113 using high-throughput sequencing technology. In
addition, we used in silico transcriptome analyses, RACE, qPCR
and conventional PCR coupled with Sanger sequencing. These approaches
successfully identified genes required for saxitoxin-synthesis in the two
transcriptomes. We focused on sxtA, the unique starting gene of
saxitoxin synthesis, and show that the dinoflagellate transcripts of
sxtA have the same domain structure as the cyanobacterial
sxtA genes. But, in contrast to the bacterial homologs, the
dinoflagellate transcripts are monocistronic, have a higher GC content, occur in
multiple copies, contain typical dinoflagellate spliced-leader sequences and
eukaryotic polyA-tails. Further, we investigated 28 saxitoxin-producing and
non-producing dinoflagellate strains from six different genera for the presence
of genomic sxtA homologs. Our results show very good agreement
between the presence of sxtA and saxitoxin-synthesis, except in
three strains of A. tamarense, for which we amplified
sxtA, but did not detect the toxin. Our work opens for
possibilities to develop molecular tools to detect saxitoxin-producing
dinoflagellates in the environment.
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Affiliation(s)
- Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
| | - Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
| | - Ralf Kellmann
- Department of Molecular Biology, University of Bergen, Bergen,
Norway
| | - Shauna A. Murray
- School of Biotechnology and Biomolecular Sciences and Australian Centre
for Astrobiology, University of New South Wales, Sydney, Australia
- Sydney Institute of Marine Sciences, Mosman, New South Wales,
Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences and Australian Centre
for Astrobiology, University of New South Wales, Sydney, Australia
- Sydney Institute of Marine Sciences, Mosman, New South Wales,
Australia
| | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
- Department of Biology, Centre for Ecological and Evolutionary Synthesis
(CEES), University of Oslo, Oslo, Norway
- * E-mail:
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