We are very happy to announce a recent reorganization of the G10K consortium and an initiation of our new reference Vertebrates Genomes Project (VGP) that we would like to get the G10K community involved in.
Some highlights of the VGP Reference project are as follows:
Interim. Based on the positive and useful lessons learned from the G10K-BGI 101 genomes project and the Avian Phylogenomics Project published in 2014-2015, after the G10K conference at the Chaminde Resort, Santa Cruz in March 2015, G10K leadership decided to focused inward with a small leadership committee that met online once/month to reorganize and develop a viable plan to achieve the primary mission of G10K.
Reorganization: We completed the reorganization in March 2017, where we now have an official G10K Chair (a position I was asked to take on and voted on), a 14-member council, associated subcommittees Genome 10K Council Members appointments and terms, and set of voted on Genome10K Consortium Bylaws.
VGP: During this two-year period, we worked with all the major genome sequencing and assemblies companies, apply all their technologies to one animal (a hummingbird; and a goat for some in a parallel effort), to determine the best path forward for generating high quality genomes.
Based on our findings we formed the reference VGP, whose mission it is to generate error-free, near gapless, chromosomal level, haplotyped phase assemblies of all ~66,000 vertebrate species. We set a minimum metric to be N50 contig >1Mb, N50 Scaffold >10Mb, >90% of genome assembled into chromosomes, and phased as much as possible. We find that such genomes are necessary for a number of analyses and its prevents a lot of errors.
See external data use policies, which explains more. These will be publicly released as part of a press release about the VGP in January 2018 at the PAG San Diego meeting.
VGP ordinal project: We have decided to pursue the reference VGP in phases of phylogenetic scale, based on species classifications (order, family, genera, and all species) and even separation of estimated divergence times between the species sequenced at each phase. We have started the ordinal phase this past summer 2017, with a few test genomes, and have subsequently made a tentative, selected list of species representing 260 lineages. The VGP selected species list is found here.
Funding and assembly pipeline: We are currently raising funds by individual citizen science contribution, and have commitments of over $2.1 million that covers approximately 1/4th of the 260 species. We have been receiving new commitments weakly. Species with both funds and samples obtained are highlighted green in columns H and I of the online list; those with funds only but in still need of a sample are highlighted yellow.
If you have such samples of~500 mg of tissue or equivalent of blood, fresh frozen, of the heterogametic sex, and wish to contribute, please let me know. Our current ordinal reference VGP genomes pipeline includes a combination of Pacbio long reads, Bionano optical maps, 10X Genomics linked reads, and HiC, and commercial as well as custom algorithms generated by Adam Phillippy’s, Richard Durbin’s, and Gene Myers labs. We have a v1 assembly approach that meets the G10K reference metric, and working on v2 that should go well above it. Much of the genome sequencing is being done at the Vertebrate Genome Lab (VGL) at the Rockefeller University, at the Sanger, and Max Plank in Dresden. The VGL was specifically built for the VGP, which I negotiated as a part of my start-up package in moving from Duke University to Rockefeller University at the end of last year (will be using Rockefeller email on this list in the future
ejarvis@rockefeller.edu). The VGL lab is directed by Olivier Fredrigo (former Duke Genome Center director) and myself. To make this project affordable, we negotiated large discounts with sequence companies for reagents and other items for the VGP (attached excel file, which shows both non-discounted and G10K discounted cost based on genome size). We have also been obtaining blanket permits for all vertebrates to transport tissue samples.
Getting involved: As with G10K, we have an open door policy for the reference VGP. If you want to get involved with sample contributions, funds, analyses, coordinate with your own genome projects, etc. please email my administrative coordinator
Lauren Shanker and she will add you to the Vertebrate Genomes Project email group. We are currently about 40 people, and expect to grow as more genomes and funds are contributed and obtained. I will send a separate email announcing the main players in the VGP.
You are also invited to attend a G10K workshop on the reference VGP at PAG on January 17th, 2018. More information about the VGP planning meeting is available here.
Welcome back!
Best,
Erich Jarvis
