Moore Notes 7 24 13

Group Call

• 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.