Wellcome Sanger Institute/Gordon & Betty Moore Foundation (New Collaboration): 2021 Aquatic Symbiosis Project – Training in Bioinformatics – Applications Due: November 1, 2020

Sun, Nov 1, 2020, 11:59 pm
Audience: 
Request for Proposals
Life Sciences
Various Research Areas

Opportunity:

The Aquatic Symbiosis Project, jointly funded by the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation, seeks to provide the genomic foundations needed by scientists to answer key questions about the ecology and evolution of symbiosis in marine and freshwater species, where at least one partner is a microbe.

By applying the latest genomic techniques and tools to 1,000 aquatic species, representing 500 symbiotic relationships, the data will guide future studies and help to inform conservation efforts. The Symbiosis in Aquatic Systems Initiative has  announced a new collaboration with the Wellcome Sanger Institute to sequence the genomes of 1,000 freshwater and marine organisms involved in aquatic symbioses where at least one partner is a microbe. The Aquatic Symbiosis Project seeks to provide the genomic foundations needed by scientists to answer key questions about the ecology and evolution of aquatic symbioses. The goals of this project are to create essential research infrastructure and to build community across aquatic symbiosis researchers.

This is a two phase project; phase one is complete.

Phase One of the Aquatic Symbiosis Genomics project has linked the Sanger research team with four international teams of collaborators who bring their expert knowledge in symbiosis to the project. The four team leads are:
Dr. Ute Hentschel Humeida (GEOMAR Helmholtz Centre for Ocean Research, Germany): Sponges as symbiont communities

  • Dr. Jose Victor Lopez (Nova Southeastern University, USA): Photosymbiosis in marine animals
  • Dr. Michael Sweet (University of Derby, UK): Coral symbiosis sensitivity to environmental change
  • Dr. John Archibald (Dalhousie University, Canada): Evolution of new symbioses in single-celled eukaryotes

 Phase Two is now open for applicants to propose additional organisms for sequencing.

In this call, the program is inviting prospective collaborators interested in leading a research hub, coordinating submission of samples of up to 50 symbiotic systems (i.e. approximately 100 species) for genome sequencing. The program expects to recruit up to six hubs. Leaders are expected to propose hubs with:

  • An explicit theme/focus, likely on a particular taxonomic group, ecosystem, and/or symbiotic process. For example, “photosynthetic symbioses of sponges” would be appropriate, as would “animal chemosymbiosis in cold seep ecosystems”.
  • Clear scientific questions related to the genomic biology of the symbioses and patterns of symbiosis across the group and/or ecosystems, and articulation of how genomics will help understand the systems.
  • A collaborative team of researchers from several institutions who will each bring specific tax of researchers who are aligned to the theme and able to supply samples from (for example) the field, laboratory or aquaria.
    • The research hub can have up to 10 named collaborators who will supply specific specimens or resources.
    • A hub could be open to onboarding of additional hub participants in the future.

The full program details and FAQ can be viewed here.

Fields of Research:

Genomics of marine aquatic symbiosis

Eligibility:

  • PIs focused in the research area who interested in leading a research hub that will coordinate submission of samples of up to 50 symbiotic systems (i.e. approximately 100 species) for genome sequencing.
  • Researchers must have permanent appointments at a university or academic research institution.
  • The program will not accept applications from students, postdocs or contractors.
  • You may apply to be the lead for one research hub.
  • You may be a team member (not lead) on one other research hub proposal.
  • There is no requirement for hubs to have deep expertise in genomics or bioinformatics, but the program will expect you to have an ambition to become competent and engaged with genomics data.

Assistance with Application: The Corporate Engagement and Foundation Relations team is available to assist faculty with proposal development and submission.  We welcome the opportunity to work with you - please call me at x8-9944 if you would like assistance.

Costs/Benefits of Participation:

  • The program will cover the costs of shipping of samples to the Sanger Institute, extraction, sequencing, assembly and primary analysis. The program cannot cover local collection costs, culturing costs or staff time for you or your collaborators.
  • For intensive in-person bioinformatics training, the program will work with research hub leaders to select one or more team member(s) associated with your hub to participate in the course. This will include access to program training and outreach programs (including access to all-expenses-paid attendance at program training and workshop events in the U.K.).
  • The introductory level online courses will be offered openly to all research hub participants.
  • The program will, within the project, assist hubs in establishing independent bioinformatics knowledge and capacity, and in building a community of interest through the aquatic symbiosis field.
  • The program will offer intensive training to selected individuals within each hub who will act as local ambassadors for the development of bioinformatics capacity, nucleate local training initiatives, and call for assistance from the Sanger Institute as needed. Where there is capacity, the program will respond to requests for training in specific analysis modalities (transcriptomics, metagenomics, epigenomics, etc) as needed.
  • The program will develop and deliver online training that can be deployed both centrally, and locally within hubs, to raise the general level of genomics and bioinformatics expertise and skills in the community.

Application:

View the program application form here.

  • Please refer to the document Aquatic Symbiosis Genomics Sanger Project_Phase2_OpenCall for full details of how to apply, including a list of FAQs.
  • The project is time limited. Potential collaborators should be mindful of the need to have their high quality biological samples with the Sanger genomics team as rapidly as possible – within 6 months of project initiation.
  • Species and samples need to be ethically sourced and compliant with the Nagoya Protocol on Access and Benefit Sharing of the Convention on Biological Diversity (i.e. come with documentation of compliance). These permissions will need to include the ability to release the assembly and sequence data openly, and to destructively sample the supplied materials. Samples lacking comprehensive sampling metadata cannot be submitted to public databases, and so we will require extensive sample source metadata to accompany each sample.
  • For additional information, please read:
  • All data will be made public on completion of primary validated assemblies.
    • The program’s data release policy follows. In summary, data will not be embargoed but the program will publish Genome Notes naming all who contribute to the generation of the sequence data (including local coordinators, collectors and lab staff, etc.) to ensure credit is ascribed correctly. These Genome Notes will not preclude subsequent publication of integrated, comparative or “deep dive” analyses.
    • To maximize the future utility of the genome data generated, collaborators are strongly encouraged to commit to making biological samples available to others where logistically feasible.
  • All sequence data generated by the project will be openly available for reuse. All raw and assembled data will be deposited in the European Nucleotide Archive (ENA) public database and from there, into the other International Nucleotide Sequence Database Collaboration (INSDC) nodes: GenBank and the DNA Data Bank of Japan. In the spirit of collaboration and community-building, the program strongly encourages research hubs to make biological materials available to others for post-genomic work. The program expects that collaborators will deposit samples relevant to the sequenced species and individuals into national and local collections (including cryorepositories). Where samples derive from cultured organisms, collaborators should, where feasible, make cultures/organisms available on request to other research labs.
  • The Sanger Institute project team encourages community reuse, and project data will be released freely for reuse for any purpose upon deposition in ENA. The intention is to rapidly publish all submitted assemblies as Wellcome Open Research notes, which can be cited (see, for example, Daniel Mead, Kathryn Fingland, Rachel Cripps et al. [2020]. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome Open Research. DOI: 10.12688/wellcomeopenres.15679.1). Scientists who use the genome sequence data are expected to give appropriate acknowledgement and citation in their own publications.
  • The Sanger Institute team will also make available for download intermediate data and assemblies via a project website. These data and assemblies are provided “as is” as a service to the community, and the team makes no assurances as to their completeness or quality. Please note that these assemblies will be improved before final submission to ENA and we cannot guarantee persistence or availability of intermediate files in the long term. The program team strongly recommends that published analyses are based on data and assemblies submitted to ENA/INSDC. The genome sequences submitted to ENA by the Sanger Institute will be presented through the EBI Ensembl database, and the annotations presented through Ensembl should be regarded as the official versions.

Please note: The Wellcome Sanger Institute is already sequencing several aquatic symbioses as part of the soft launch of this program. Please refer to the list of organisms already in the sequencing queue in the Aquatic Symbiosis Genomics _ Species list Phase 1. The team encourages you to consider other species in your application to maximize representation across the tree of life. Please email masg@sanger.ac.uk for additional information or questions.

Due Dates:

  • Applications are due November 1, 2020 at 11:50 p.m. PT
  • Applicants will be notified of a decision by mid-December 2020.
Categories: Open Call RFPs