A plan to build a Noah's genetic ark includes 66,000 species

An international consortium of more than 50 institutions has announced an ambitious project to bring together high-quality genomic sequences from 66,000 vertebrate species on Earth, including all mammals, birds, reptiles, amphibians and fish. With a total estimated cost of $ 600 million, it is a project of biblical proportions.

It is called the Vertebrate Genomes Project (VGP) and is organized by a consortium called Genome 10K or G10K. As the name suggests, this group originally planned to sequence the genomes of at least 10,000 vertebrate species, but thanks to the considerable progress made and cost savings in genetic sequencing technologies, G10K has decided upon and female individuals from each of the 66,000 species of vertebrates on Earth.

The project's co-founders announced the new goal yesterday at a press conference held at the opening session of the 2018 Genome 10K conference, currently being held at Rockefeller University's New York. The project will involve more than 150 experts from 50 institutions in 12 countries.

The announcement comes with the publication of 14 new high-quality genomes for species representing the five classes of vertebrates, including the genome of the great bat, the Canadian lynx, the platypus, the hummingbird, and the Anna, the kakapo (only 150 survivors). individuals), the Goode Desert Turtle, the two-line Cecilian (a strange limb-less amphibian that resembles a snake) and the climbing perch. These 14 genomes, as well as those compiled during the project, will be made available to scientists for research purposes.

In fact, the VGP is not limited to the sequencing of animal genomes. Like the human genome project, this effort will undoubtedly lead to breakthroughs in high-resolution sequencing and genome-assembly methods, while reducing costs and errors. The project will also address important issues in biology and disease and will have immediate impacts on the areas of evolution, genomics and conservation biology. On this last point, a comprehensive catalog of vertebrate species on Earth could serve as a protection against extinction, both in terms of preventing extinction and possibly reviving extinct species in the future.

Speaking at the press conference yesterday, Oliver Ryer, co-founder of G10K and director of the San Diego Zoo Institute for Conservation, said the VGP had the potential to "transform all areas of biology." reasons for extinction, including the presence of deleterious mutations, inbreeding and genetic bottlenecks. For example, Ryer described the discovery of a deleterious recessive gene in California condors, stating that "we can now identify birds with this lethal trait." In the end, the project will make us "better guardians of life on Earth" and allow us to "preserve our biological heritage".

When the G10K was launched 10 years ago, its members had no idea how long it would take to sequence genomes of sufficient quality to make good science and do it at an affordable price.

"I am incredibly excited that we are now able to do things right," said David Haussler, co-founder of the G10K and director of UC Santa Cruz Genomics Institute yesterday. "It's really time to start," he adds, "we have no excuse for not doing it".

To generate high quality genome assemblies, the VGP team insists on "long readings" rather than "short reads," which means that sequencing technologies produce longer pieces of contiguous genetic data. will be privileged. This will greatly facilitate the assembly of DNA sequences into whole chromosomes. Thus, instead of working with a puzzle containing millions of pieces, the long readings will give rise to a puzzle composed of thousands of pieces.

In addition, researchers will refrain from combining male and female chromosomes into a single genome – a common practice that causes far too many errors. Instead, the team will gather both paternal and maternal DNA from individuals in a process known as phasing. As Gene Myers, a member of the VGP team and senior scientist at the Max Planck Institute for Molecular Cell Biology and Genetics, said yesterday, each species will be a "unique" agreement, meaning that the quality of sequences will be so good. that work should not be repeated in the future. In this way, "we can continue with science," he said.

In terms of process, researchers will construct long read sequences with an initial assembly of chromosome pieces called "contigs". These pieces will come together to create even larger pieces, called scaffolding, which will in turn be linked to others to create even larger assemblages, up to normal size chromosomes. Optical DNA maps and computer algorithms will facilitate the process, ensuring the proper sequential order and signaling any structural errors.

"Advances in long-reading sequencing and long-range scaffolding technologies are revolutionizing [starting from scratch] Sequencing of DNA, "said Myers. "After a 10-year hiatus, this trend has encouraged me to go back to the genome assembly, because I think we will eventually be able to produce near-perfect reconstructions of the telomere and telomere genome, and if current trends hold for less than $ 1,000. on average per vertebrate species, thus dramatically changing the landscape of genomics.

In fact, not so long ago, it took millions of dollars and years of effort to complete the genome of a single animal. New sequencing technologies may soon be able to create an entire genome in a week, said Adam Phillippy, chair of the G10K assembly and head of the NIH's National Institute for Human Genome Research. It now takes about $ 30,000 to sequence the DNA of a new species for the first time.

The new sequences will be stored and made available to the public on the Genome Ark database, an open digital library of genomes. The DNAnexus and Amazon Web sponsor companies "played a key role in this project," Phillippy said.

"This project is extravagant and outrageous – but it's feasible, and it's inevitable," said Harris Lewin, a member of the UC Davis VGP team, at the press conference.

According to a G10K press release, approximately $ 600 million will be needed to complete all phases of the VGP. To fund the project, G10K acquires money from private institutions and corporate sponsors. But the consortium is also crowdsourcing, having already raised $ 2.5 million out of the $ 6 million required for the first phase of the project (the first phase will involve the sequencing of at least one individual among the 260 orders of live vertebrates).

Aside from hyperbole, this is one of the most ambitious projects we've seen in a long time, rivaling the Human Genome Project (HGP), the Connectome Human Project (a continuing effort to map all brain connections The twin VGP project, the Earth BioGenome Project (EGP), announced earlier this year. The goal of the EGP is to sequence all eukaryotes (there are about 8.7 million species on the planet), at an estimated cost of $ 4.7 billion. In an e-mail to Gizmodo, a G10K spokesperson said that EGP will function as a coordinating body and that VGP's vertebrate genomes will contribute to the overall effort to eliminate labor replication.

No timetable has been given for the VGP project, but as demonstrated by the HGP, a slow start does not necessarily reflect the overall pace of a project. As time goes on and technologies and techniques improve, VGP researchers should start to see faster returns, both in terms of speed and cost reduction. Once completed, we will have a remarkable deposit at our disposal, which even Noah would be proud of.