i5K Coordinating Group

Conference Call Agenda

Feb 21, 2018

10:00-11:00 (EST)

Considerable time has elapsed since our November meeting; we need to re-visit on-going efforts and determine what we will focus on in 2018. One focus will likely be on positioning i5K to take advantage of potential funding opportunities resulting from the Earth BioGenome Project and other global or local genomics efforts.

Attending: Monica Poelchau, Anna Childers, Chris Childers, Kevin Hackett, fringy Richards, Denis Tagu, Marian Goldsmith, Jay Evans, Brad Coates, Gene Robinson

  • I5K Pilot: Status and Future (fringy)
    • Working on i5k pilot paper:"Genomic innovation across the arthropods". Also added some other species outside the i5k pilot group. The group is looking at GC content and protein domain change. Will try to wrap paper up in next month.
    • Also working on lateral gene transfer pipeline with Jack Werren, might run that on the pilot species. Ran Jack's scripts on 100 assemblies. Trying to automate what Jack does in Excel.
  • EBP Update (Gene, Kevin, fringy, Jon)


    • Next planned EBP workshop will be postponed
  • Nominations for Core i5K Taxonomic Groups (fringy, Anna). Immediate goal is to develop prioritized lists of species that cover all Arthropod families
    • i5k Species Nomination Database Update: COIS (fringy)
    • COIS issue: reviews on each of the major holometabolous orders, also spiders. 8 reviews plus intro. A good description of where the field is now.
      • Arachnids, Hymenoptera, Ants, Beetles, GGI/GGBN, Lepidoptera, Hemiptera, Diptera. No Crustacea, basal insects, Myriapods, Chelicerates (though some highlights in Arachnid review)
    • Issue is not quite finalized, but most papers are up on the COIS website. Anna will try to publicize them a bit more.
    • Collecting teams for each issue helped spread out the work for each review.
    • Failed on the idea of a quantitative list – didn't solve the i5k question of getting a list; only a few numbers/species specifically listed.
    • Kevin: COIS2? Insect genomics section is every 2 years – might be nice to revisit in 2 years. We could perhaps petition the members of the board, but need to make a compelling case.
    • Kevin: we need to continue to discuss nominations. Not sure how to entice individuals into nominating species, unless there's money involved.
    • For 'the list' – we're not seeing willingness to consider nominations on a global scale, but instead nationalizing collections (all species in country X).
  • Funding
    • NHGRI-February (fringy)
      • Comparative genomics grant; next deadline is June. It's an R01, 3 year, capped at 500k/year (but could petition for more than the cap). Sequence non-human species; aiming at understanding biology through comparative genomics.
      • Initial idea: focus on 500-1000 holometabolous insects (small genomes); associate gene content with interesting phenotypes that would be of interest to NHGRI. (e.g. long-lived and short-lived species; find trios where one has changed in life span significantly, repeat many times; find which pathways have changed between long-lived and short-lived species. Genomics of cancer?).
      • To reduce costs: originally thought to do 10x genomics (costs have dropped, could use MiSeq). Could do oxford nanopore Promethion, instead. Might have to go for long-read genomes instead of draft genomes. The catch is fringy can't do this at Baylor anymore; fringy can't take over the sequencing part.
      • It makes a difference to have 'the species list' already available for the grant proposal (to convince reviewers that samples are available).
      • Kevin: major weakness of i5k is willingness to write grant proposals.
      • Kevin: Perhaps pathogen transmission would be a good phenotype? Could you team up with the vertebrate folks and do a host/pathogen proposal?
      • Anna: if we could align with V10k could team up with Adam Phillipy and use oxford nanopore.
      • Gene: Is Sue interested in writing? Mike and Gene have been talking about a separate NSF proposal.
      • Perhaps industry funding (plant and Ag biotech)? Kevin: Gene, Sue, Kevin tried to cobble together industry funding a while back and failed because only BASF pitched in. Have things changed enough to try again (industry and scientific landscape) – does it make sense now to pool resources for more genomes? Anna – should we look to growers (e.g. citrus industry as a model)? Does ESA have some kind of industry partnership group? Can we make the argument that we'd be more efficient at sequencing 500 genomes than industry would? Industry could possibly benefit from more sequences to work with. Brad: looks like industry is getting more interested in population genetics due to resistance evolution. Gene: Monsanto is still hunkered down and worried about the merger; there might not be an appetite to try something totally new.
  • Other Business
    • Denis: European training network opportunity: grant for 15 PhD students. Program is about invertebrate genomics/transcriptomics, coordinated by a German PI in Munich (GIGA). There are 14-15 labs all over Europe that are now offering these positions. This is a training network, so students will have co-supervisors in another lab of the network. Students can move between labs to learn new techniques. There will be summer schools, workshops, etc. for training. Deadline for students is at the end of February, students will be selected started in April. These are 3-year positions. You don't have to be an EU citizen to apply. http://www.itn-ignite.eu/projects/

NEXT MEETING: March 28th, 2017

10:00-11:00 am EST