Project Info: Overview
The Broad Institute, Marine Microbiology Initiative (MMI) at the Gordon & Betty Moore Foundation, and selected research groups are collaborating to sequence, assemble, and annotate approximately 200 diverse marine phage/virus genomes and to sequence approximately 50 viral metagenomes from an array of marine environments. This project follows on the successful development of a cyanophage genome sequencing and annotation pipeline developed at the Broad Institute with support from MMI. The current effort takes advantage of this pipeline and will greatly enhance the amount of available genomic and metagenomic information about marine phage and viruses with the broader goal of illuminating the ecology and evolution of not just the phage and viruses themselves, but also of the bacteria, archaea and unicellular eukaryotes they infect.
This scope of this project was developed in large part based on an international needs assessment conducted in 2008 and will support a limited number of 454 Titanium pyrosequencing runs to generate approximately 200 phage/virus genome sequences and approximately 50 viral metagenomic datasets. The spread of genome sizes will range from as small as ~20 kb to over 400 kb, with no specified maximum phage/viral genome size accepted into the pipeline. All phage/viral nucleic acid types are acceptable. After passing the Broad Institute's quality control steps, genome samples will be sequenced, assembled and annotated using a newly developed protocol at the Broad Institute, as is feasible, whereas virome sequence reads will be provided to collaborating researchers for contig assembly and annotation. Genome sequencing is expected to result in single contigs of at least 15X coverage, although the final results depend on many factors. Collaborating researchers are also required to supply oceanographic and other metadata relating to their samples. After a six month embargo, all sequences and associated metadata will be released publicly at the CAMERA sequence repository and analysis platform (Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) and at NCBI.