Project to read genomes of all 70,000 vertebrate species reports first discoveries

(Press-News.org) It's one of the most audacious projects in biology today - reading the entire genome of every bird, mammal, lizard, fish, and all other creatures with backbones.

And now comes the first major payoff from the Vertebrate Genome Project (VGP): near complete, high-quality genomes of 25 species, Howard Hughes Medical Institute (HHMI) Investigator Erich Jarvis with scores of coauthors report April 28, 2021, in the journal Nature. These species include the greater horseshoe bat, the Canada lynx, the platypus, and the kākāp? parrot - one of the first high-quality genomes of an endangered vertebrate species.

The paper also lays out the technical advances that let scientists achieve a new level of accuracy and completeness and paves the way for decoding the genomes of the roughly 70,000 vertebrate species living today, says HHMI Investigator and study coauthor David Haussler, a computational geneticist at the University of California, Santa Cruz (UCSC). "We will get a spectacular picture of how nature actually filled out all the ecosystems with this unbelievably diverse array of animals."

Together with a slew of accompanying papers, the work is beginning to deliver on that promise. The project team has discovered previously unknown chromosomes in the zebra finch genome, for example, and a surprise finding about genetic differences between marmoset and human brains. The new research also offers hope for saving the kākāp? and the endangered vaquita dolphin from extinction.

"These 25 genomes represent a key milestone," explains Jarvis, VGP chair and a neurogeneticist at The Rockefeller University. "We are learning a lot more than we expected," he says. "The work is a proof of principle for what's to come."

From 10K to 70K The VGP milestone has been years in the making. The project's origins date back to the late-2000s, when Haussler, geneticist Stephen O'Brien, and Oliver Ryder, director of conservation genetics at the San Diego Zoo, figured it was time to think big.

Instead of sequencing just a few species, such as humans and model organisms like fruit flies, why not read the complete genomes of ten thousand animals in a bold "Genome 10K" effort? At the time, though, the price tag was hundreds of millions of dollars, and the plan never really got off the ground. "Everyone knew it was a great idea, but nobody wanted to pay for it," recalls HHMI Investigator and HHMI Professor Beth Shapiro, an evolutionary biologist at UCSC and a coauthor of the Nature paper.

Plus, scientists' early efforts at spelling out, or "sequencing," all the DNA letters in an animal's genome were riddled with errors. In the original approach used to complete the first rough human genome in 2003, scientists chopped up DNA into short pieces a few hundred letters long and read those letters. Then came the fiendishly difficult job of assembling the fragments in the right order. The methods weren't up to task, resulting in misassemblies, major gaps, and other mistakes. Often it wasn't even possible to map genes to individual chromosomes.

The introduction of new sequencing technologies with shorter reads helped make the idea of reading thousands of genomes possible. These rapidly developing technologies slashed costs but also reduced quality in genome assembly structure. Then in 2015, Haussler and colleagues brought in Jarvis, a pioneer in deciphering the intricate neural circuits that let birds trill new tunes after listening to others' songs. Jarvis had already shown a knack for managing big, complex efforts. In 2014, he and more than a hundred colleagues END