A collaboration between the National Center for Genome Resources, the Gordon and Betty Moore Foundation's Marine Microbiology Initiative, and the international marine microbial eukaryote research community sequenced the transcriptomes of 678 samples from hundreds of diverse organisms

Marine microbial eukaryotes are found in all major eukaryotic branches of the evolutionary tree. They perform a diverse range of functions in marine ecosystems-including photosynthesis, predation and parasitism. Despite the great abundance of microeukaryotes in the ocean, their importance as absorbers of carbon dioxide and their critical contribution to marine food webs (among many ecological roles), the gene content of these microorganisms is only beginning to be explored because their genomes can be structurally complex and many gigabases in size. This program is intended to increase the research community's baseline of scientific knowledge by creating catalogues of genes that specify how these organisms thrive in diverse marine habitats and how they influence marine ecosystems, biogeochemical cycles and the composition of the atmosphere.

The National Center for Genome Resources (NCGR) and the Gordon and Betty Moore Foundation's (GBMF) Marine Microbiology Initiative (MMI) are engaged in a new research collaboration with the international marine microbial eukaryote research community to sequence the transcriptomes of approximately 750 samples that are expected to represent hundreds of diverse species and strains. Transcriptomes will be generated de novo using the Illumina HiSeq 2000 platform.

This project aims to significantly enhance the research community's ability to:

  1. Explore the physiology of diverse marine microbial eukaryotes;
  2. Interpret metagenomic and metatranscriptomic data generated from marine ecosystems; and
  3. Illuminate the evolutionary relationships among marine microbial eukaryotic clades and within the overall eukaryotic tree of life.

MMI and NCGR are soliciting nominations for transcriptome sequencing from the international scientific community, which will be reviewed by a panel of five experts. Sequencing nominations may target diverse microeukaryotes for which little or no gene content information exists and/or include comparative transcriptomic experiments.

To meet the project aims noted above, the expert panel will consider nominations that:

  1. "Fill in the blanks" on the evolutionary tree of microeukaryotes using transcriptome sequencing of cultured organisms; and
  2. Target deeper exploration of marine microeukaryotes that are known to play important ecological roles.

A very limited number of non-marine microeukaryote nominations may be accepted should the proposing researcher make a strong case for how the transcriptome sequencing will significantly increase the research community's understanding of marine microbial eukaryotes. However, nominations for environmental metatranscriptomic sequencing (e.g. of a flow sorted population) or whole genome sequencing will not be accepted.

Time Line:

December 20, 2010 Nominations due via NCGR on-line nomination portal
February, 2011 NCGR notifies researcher of decision
3 months following notification Sample submission to NCGR*

* Time extensions may be requested due to organisms that are known to grow slowly and/or if a researcher has many samples to prepare. Samples will be placed in NCGR's sequencing queue and processed on a first-come, first-served basis.

For accepted nominations, specific instructions for submitting RNA and the time line for subsequent sequencing-related milestones (e.g. sample quality control checks; completion of sequencing) will be provided to the researcher by NCGR at the time of notification.

For samples accepted into the project, environmental and experimental metadata must be submitted to NCGR before sample submission kits will be sent to a researcher's laboratory. Transcriptome sequence datasets, assemblies, annotations and associated metadata will be deposited in the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) and the Short Read Archive at the National Center for Biotechnology Information. Because the data generated for this project will serve as a resource to the entire the research community, all sequence information and associated metadata will be made publicly available six months after the researcher who submitted a sample receives his/her data. Please see Resources for details on accessing data.

For questions, please visit the Frequently Asked Questions.

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