Reference Vertebrate Genomes Project (VGP)
The Vertebrate Genomes Project (VGP), a project of the G10K Consortium, aims to generate near error-free reference genome assemblies of all 66,000 extant vertebrate species. These genomes will be used to address fundamental questions in biology and disease, to identify species most genetically at risk for extinction, and to preserve genetic information of life. The motivation for the VGP is based in part on the G10K mission to generate genomes of 10,000 or more vertebrate species and on lessons learned from The Avian Phylogenomics Project.
December 11, 2017
Dear G10K Scientist and Affiliates,
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.
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.
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.