Moore Notes 7 24 13
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- Participants: Katie, Jonathan, Ladan, Sarah, Dongying
- Josh's visit to Davis went well. Great talk. He should go on the job market.
- VIROME: Eric Wommack
- Virus diversity
- Developed a bioinformatics pipeline because there weren't tools out there
- Primarily a virus biologist, oceanographer
- How applicable are VFams to marine microbiology?
- Many sequenced viruses have mammalian or well-characterized bacterial hosts
- Eric probably mostly interested in phage
- Giant viruses are mostly marine
- If some one does size fractioning, then these will end up in bacterial and eukaryote fractions
- Their genomes are very divergent
- What about eukaryote protein families?
- Tom and/or Holly may want to work on this
- Eukaryotic diversity is bad in genome databases
- Should have photosynthetic algae (not closely related to plants), but none have genomes yet
- Could be a good test case for seeing how using metagenomes or assemblies from metagenomes work for building protein families
- Good options for interactions with other GBMF labs
- Ambrose is doing some diatom genomes, which could be used for validation of the metagenome-based families idea
- EMP samples
- Talked with Jack Gilbert last week
- Got quote for sequencing with them
- Jonathan will get a quote from BGI, his lab could potentially do the library prep
- Jack's group will be sending information about samples
- Would be cool to do coastal, but environmental rasters are probably not fine enough resolution
- Open ocean, maybe geographically restricted (e.g., the pacific), would be better
- Interesting article: http://www.bath.ac.uk/news/2013/07/24/small-organisms-species/
- Organism size as proxy for population size?
- Recombination rates
- Thinking about how this relates to the human microbiome popgen paper by Bork, Weinstock, et al.