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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List

Grants

Courtesy of Marine Microbial Eukaryote Transcriptome Project, diatom frustule

National Center for Genome Resources

Marine Microbial Eukaryote Transcriptome Sequencing Project

To support the National Center for Genome Resources to sequence and perform initial characterizations of the gene content of hundreds of diverse marine microbial eukaryotes. The resulting sequence data and associated metadata are publicly available.

Title: Marine Microbial Eukaryote Transcriptome Sequencing Project
Date Awarded: Sep 2010
Amount: $2,361,955
Term: 40 months
Grant ID: GBMF2637
Funding Area: Science, Marine Microbiology Initiative

Marine microbial eukaryotes form a foundational component of the evolutionary, food web and biogeochemical processes in the ocean. While these highly diverse organisms are typically 10-100 times less abundant than marine bacteria and archaea (and ten times further less abundant than marine viruses), they dramatically influence the diversity, ecology and evolution of nearly all marine microbial communities. Further, these microbes perform highly varied ecosystem functions, ranging from photosynthesis, heterotrophy and predation to parasitism. Only recently have studies emerged to evaluate the gene content and genomic attributes of these unique organisms to better understand their diversity and ecology. Such studies are only now possible with deep sequencing technology primarily due to the structurally complexity and extensive genome size of marine eukaryotic microbes (some of these genomes significantly dwarf the human genome). 

The National Center for Genome Resources (NCGR), the Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation and the international marine microbial eukaryote research community have recently completed a collaborative effort to sequence the transcriptomes (the expressed gene content from the genome) of more than 650 samples representing hundreds of diverse species and strains. The effort provides a means to “fill in the blanks” on the eukaryotic evolutionary tree of cultured organisms, and rounds out MMI’s sequencing portfolio, which also contains the Microbial Genome Sequencing Project to sequence diverse marine bacterial and archaeal cultured isolates; the Marine Phage, Virus and Virome Sequencing Project to sequence viral isolates and viral metagenomes; and the Environmental Metagenomics Sequencing Portfolio to sequence whole microbial communities from locations around the world.

The MMETSP will enable researchers to deepen current understanding of microeukaryote ecology, nutritional strategies, evolution and roles in marine biogeochemistry. Moreover, this unique datasets will have far-reaching impact beyond the field of marine microbial ecology, providing a wealth of data which will transform current understanding of the basic biology of these organisms. Further information about the project is available through NCGR’s project webpage http://marinemicroeukaryotes.org/.

Activities

The following workshops and conference sessions have highlighted the Marine Microbial Eukaryote Transcriptome Sequencing Project, and have helped researchers exchange ideas, learn new bioinformatics methods and forge new collaborations.

MMETSP Special Session at the Joint ISOP/ISEP Protist 2014 Conference, August 3-8, 2014, Banff, Alberta, Canada

Microeukaryote Bioinformatics Workshop on Analyzing Protist Transcriptomes at the International Congress of Protistology XIV Meeting, July 31, 2013, Vancouver, British Columbia, Canada (Available workshop resources)

ASLO 2013 Aquatic Science Meeting Town Hall - Marine Microbial Eukaryote Transcriptome Project, February 16, 2013, New Orleans, LA, USA

Past activities also included a bioinformatics internship program for participating research labs involved with the MMETSP hosted by staff at NCGR. The eight week summer program included two weeks of teaching and hands-on learning (lecture format plus computer lab), followed by six weeks for the interns to pursue independent research projects based on the MMETSP data generated at NCGR.

Bioinformatics Resource

A bioinformatics platform PhyloMETAREP (http://www.jcvi.org/phylo-metarep/) has been supported (Grant #2900; PI: Dr. Andy Allen) to enable exploration, visualization, and comparisons across annotated marine eukaryote transcriptomes. A key component of the PhyloMETAREP platform is a custom database, PhyloDB, which consists of manually annotated nuclear and organelle reference genomes and gene expression profiles suitable for genomic analyses of marine microeukaryotes and other microbes.

Data Availability

All data are publicly available as listed below.

Assembly Type Raw Reads  Assembled Contigs  CDS  Peptides  Annotations   Read Counts Metadata 
 Single  a,c  a  a  a  a  a  a,c
 Combined  NA*  b  b  b  b  b  b

 

a. CAMERA http://camera.calit2.net/mmetsp/list.php

b. CAMERA http://camera.calit2.net/mmetsp/combinedassemblies.php

c.  SRA http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA231566

*The combined assemblies originate from reads from the single assemblies 

Publications as of July 2014

  1. Keeling, P. J., F. Burki, H. M. Wilcox, B. Allam, E. E. Allen, L. A. Amaral-Zettler, E. V. Armbrust, J. M. Archibald, A. K. Bharti, C. J. Bell, B. Beszteri, K. D. Bidle, C. T. Cameron, L. Campbell, D. A. Caron, R. A. Cattolico, J. L. Collier, K. Coyne, S. K. Davy, P. Deschamps, S. T. Dyhrman, B. Edvardsen, R. D. Gates, C. J. Gobler, S. J. Greenwood, S. M. Guida, J. L. Jacobi, K. S. Jakobsen, E. R. James, B. Jenkins, U. John, M. D. Johnson, A. R. Juhl, A. Kamp, L. A. Katz, R. Kiene, A. Kudryavtsev, B. S. Leander, S. Lin, C. Lovejoy, D. Lynn, A. Marchetti, G. McManus, A. M. Nedelcu, S. Menden-Deuer, C. Miceli, T. Mock, M. Montresor, M. A. Moran, S. Murray, G. Nadathur, S. Nagai, P. B. Ngam, B. Palenik, J. Pawlowski, G. Petroni, G. Piganeau, M. C. Posewitz, K. Rengefors, G. Romano, M. E. Rumpho, T. Rynearson, K. B. Schilling, D. C. Schroeder, A. G. Simpson, C. H. Slamovits, D. R. Smith, G. J. Smith, S. R. Smith, H. M. Sosik, P. Stief, E. Theriot, S. N. Twary, P. E. Umale, D. Vaulot, B. Wawrik, G. L. Wheeler, W. H. Wilson, Y. Xu, A. Zingone, & A. Z. Worden. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol, 12(6), e1001889. doi: 10.1371/journal.pbio.1001889
  2. Rockwell, N. C., D. Duanmu, S. S. Martin, C. Bachy, D. C. Price, D. Bhattacharya, A. Z. Worden, & J. C. Lagarias. (2014). Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci U S A, 111(10), 3871-3876. doi: 10.1073/pnas.1401871111 
  3. D'Adamo, S., R. E. Jinkerson, E. S. Boyd, S. L. Brown, B. K. Baxter, J. W. Peters, & M. C. Posewitz. (2014). Evolutionary and biotechnological implications of robust hydrogenase activity in halophilic strains of tetraselmis. PLoS One, 9(1), e85812. doi: 10.1371/journal.pone.0085812
  4. Koid, A., Z. Liu, R.Terrado, A. C. Jones, D. A. Caron, & K. B. Heidelberg. (2014). Comparative Transcriptome Analysis of Four Prymnesiophyte Algae. PLoS One, 9(6), e97801. doi: 10.1371/journal.pone.0097801.t001 
  5. Imanian, B., & P. J. Keeling. (2014). Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms. Genome Biol Evol, 6(2), 333-343. doi: 10.1093/gbe/evu014 
  6. Bender, S. J., C. A. Durkin, C. T. Berthiaume, R. L. Morales, & E. V. Armbrust. (2014). Transcriptional responses of three model diatoms to nitrate limitation of growth. Frontiers in Marine Science, 1. doi: 10.3389/fmars.2014.00003
  7. Tanifuji, G., N. T. Onodera, M. W. Brown, B. A. Curtis, A. J. Roger, G. Ka-Shu Wong, M. Melkonian, & J. M. Archibald. (2014). Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics, 15, 374. doi: 10.1186/1471-2164-15-374 
  8. Adelfi, M. G., M. Borra, R. Sanges, M. Montresor, A. Fontana, & M. I. Ferrante. (2014). Selection and validation of reference genes for qPCR analysis in the pennate diatoms Pseudo-nitzschia multistriata and P. arenysensis. Journal of Experimental Marine Biology and Ecology, 451, 74-81. doi: 10.1016/j.jembe.2013.11.003
  9. Santoferrara, L. F., S. Guida, H. Zhang, & G. B. McManus. (2014). De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PLoS One, 9(7), e101418. doi: 10.1371/journal.pone.0101418
  10. Grant, J. R., & L. A. Katz. (2014). Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data. PLoS Curr, 6. doi: 10.1371/currents.tol.c24b6054aebf3602748ac042ccc8f2e9