i5K Coordinating Group
Conference Call Notes
May 20, 2020
Attending: Kristen Panfilio, Anna Childers, Chris Childers, Kevin Hackett, Rob Waterhouse, Stephen Richards, Bob Miller, Surya Saha, Monica Poelchau, Meg Allen, Xinhai Ye, Brad Coates, Jay Evans, Glenn Hanes, Dorith Rotenburg, Brian Scheffler, Mike Pfrender
EBP Update (fringy, Gene)
- Fringy: things are progressing as well as they can without lab work, but of course things are going slowly; Sanger has been generating amazing genomes on arthropods using HiC and PacBio, so hopefully we'll see more once restrictions are over. Standards calls through June to consolidate standards and put up on the EBP website. Not sure what will happen with the US bioeconomy bill given the coronavirus situation.
- Kevin: working with OSTP to move the bioeconomy bill along. Not sure what the funding status will be next fiscal year – it could go any number of ways.
- EBP IT/Infrastructure Subcommittee (Monica)
- Survey link: https://docs.google.com/forms/d/e/1FAIpQLSc11FJ5EIkV2Zn3HXuFklM0-AfybBbsM-wlZ57m_-98nBDUqA/viewform?usp=sf_link
- Other than that, this subcommittee has not met
- Other subcommittees have also been slow due to coronavirus
- Project Database (Mark, Mara, fringy, Monica): ENA-based
- Monica will connect fringy and Xinhai about project status
- Probably easiest to work with groups that are doing 100+ at a time, and genomes that will be sequenced within about a year's time (e.g. that are funded)
- ESA-Orlando (Monica, Brad)
- Still organizing the symposium, all slots are filled. How it will happen is still up in the air due to covid-19
- PAG Ag100Pests Talks (Anna, Surya)
- No updates
- AGS (Rob, Sue): Summer Meeting
- Rob, Anna, Mike and Sue have been coordinating, possibly for a 3-day, 3 hour/day meeting; and/or increase the frequency of the i5k webinars. 3 hour blocks would capture Europe evening/US East coast mid-day/US west coast time morning zones. Sessions would be organized around themes. Unsure what attendance would be – specialized sessions could attract more specialized crowds. Unsure who has access to what technology – Glenn may have access to a zoom account with a 350 limit. Rob is also already organizing another virtual conference in June.
- ICE speakers from Rob's session are interested in participating, and he is reaching out to other chairs
- What will happen will depend on the effort required from the organizers. Increasing the frequency of the webinars will probably be the least work. A virtual symposium would be more organizational work.
- If anyone has ideas for speakers, let Rob know
- Feedback on format:
- Smaller blocks would be easier for people to attend.
- Having it in 3-hour bursts may make it a bit more 'special', and it may make this more accessible for others that are more travel-challenged.
- Surya can help managing the sessions, if they come together
- Breakout rooms – the host can allow breakout rooms for smaller rooms, or participants can control those themselves, in parallel with the talks. Breakout rooms could be a unique feature.
- Themed breakout rooms (e.g. Ag100Pest) – could have a designated person remotely managing this
- Might be better to keep it simple; and if it seems like breakout rooms may have been useful, could work on building this out next time
- ESA-Orlando (Monica, Brad)
- Project Updates
- DToL (Mark, Mara)
- Ag100Pests, include Desert Locust (Anna)
- Anna: Murder hornets – they have a sample, are evaluating DNA quality. Communicating with APHIS and others to acquire fresh samples
- Desert locus: project is progressing, hopeful that funding will come through
- Overall Ag100Pest: testing PacBio ultra-low input protocol as one of 3 main collaborators; testing a single parasitoid. Can expect the same standards with ultra-low input, but still single insect may be possible. Getting great assemblies with PacBio + HiFi scaffolding. Anna will update list on i5k website soon. Her group has been able to continue sequencing and hopes to get the majority sequenced by the end of the FY.
- Beetles (Duane)
- Cornome (Brad, Jay, Dave)
- Bees (Brian)
- France (Denis)
- California Ecosystem (fringy)
- California project is starting move with species important to California.
- Li Fei's lab/Xinhai Ye:
- Agricultural pests, some natural enemies such as parasitoid wasps
- About 20 sequenced species; mostly rice pests. Includes fall army worm, coddling moth, three planthoppers, cotton mealy bugs.
- Technologies: PacBio (probably CLR), Illumina, Hi-C
- 10 species of parasitoid wasps - Working with Jack Werren at Rochester on evolutionary genomics studies.
- China has an insect sequencing committee that meets like i5k – they know who is sequencing what. What can we do to coordinate, and share data? Best thing is to get into INSDC databases, pre-publication. Advertise via portals that are coming online
- Expanding the Membership on the i5K Steering Committee (Rob)
- Invited member Kristen Panfilio specializes on evo-devo in Tribolium, led the Oncopeltus fasciatus i5k pilot project
- Invited member Dorith Rotenberg specializes on vector biology, led the Frankliniella occidentalis i5k pilot project
- survey from Mara on the highest priority UK arthropod survey: https://docs.google.com/forms/d/e/1FAIpQLSc4MHYARYl_8yuF9HoGzoN8pk9uLcXtkLL_VM2wn8-yYYLXMQ/viewform. Anna and Rob are retweeting this, and sent to AGS listserv
- Insect genomics special issue: Submissions are welcome, more info here: https://www.mdpi.com/journal/insects/special_issues/insect_genomics
- We will probably move to zoom next month, stay tuned!
NEXT MEETING: June 17, 2020
11:00-12:00 am EDT