An effort to understand the full genetic makeup of more than 70,000 mammals, birds, reptiles, amphibians and fishes has taken some major steps forward, with scientists unveiling the DNA sequences of 25 species including the Canada lynx, platypus, and zig-zag eel.
What's more, in a series of reports published in this week's Nature and other journals, researchers show that their strategies for figuring out an animal's DNA sequences can produce high-quality results with far fewer errors than earlier techniques.
The refined tools revealed genes and even whole chromosomes that had been overlooked in the past, says Erich Jarvis, a researcher at Rockefeller University. It turns out that zebra finches — songbirds key to the understanding of vocal learning in birds and people — have seven more chromosomes than previously thought, for example, and platypuses have eight more.
"People thought these genes were missing in birds and platypus, right? But they weren't missing. They just weren't sequenced with the older technologies," says Jarvis, who serves as chair of the Vertebrate Genomes Project, a group of hundreds of scientists dedicated to producing the complete genetic sequence for each of the 71,657 named vertebrate species alive today.
The work started in 2009 as the G10K consortium, which aimed to sequence the genomes of 10,000 vertebrate species to better understand their biology and how it evolved. In recent years, as technology has advanced and costs have gone down, the researchers' goals grew more ambitious. The project ultimately hopes to sequence the genomes of 125 species per week. Right now, says Jarvis, "we're doing six per week."
Importantly, their strategy separates chromosomes that an animal inherited from its mother from those chromosomes that came from the father. "Before this, almost all genome assembly approaches were taking the mother and father's chromosomes and merging them into one," says Jarvis, explaining that this can create an illusion of extra genes that don't actually exist.
Past work on receptors for the "love hormone" oxytocin, for example, incorrectly identified additional genes for these receptors in various lineages of animals "because the darned genome assemblers didn't separate Mom and Dad's DNA," says Jarvis. "So we thought we had more genes than what we really do have across all these lineages, because there were false duplications."
Looking at the maternal and paternal DNA separately allowed researchers to produce much more detailed genetic sequences for marmosets, which are an important lab monkey used to study neurodegenerative brain diseases, says Guojie Zhang, a researcher at the University of Copenhagen.
"We've now produced a highly complete genome," says Zhang, whose team looked at 2,533 genes related to brain development and disease and found that most were highly similar between humans and marmosets. A few dozen showed differences, however, that may underlie the brain differences between people and this lab animal.
The newly published genomes also include wild species currently at risk, such as the critically endangered kakapo of New Zealand, and the Canada lynx, which is listed as a threatened species in the U. S. The lynx whose DNA was used to generate the genome was caught accidentally by a fur trapper in Maine and later released with a radio collar, says Tanya Lama, a postdoctoral research fellow at SUNY Stony Brook University. "He's still out there and he's doing well," says Lama. "He doesn't know that he's famous."
The lynx genome has already offered hints of how this species might adapt — or not — to climate change, she says, because evidence in its DNA suggests that its circadian genes get regulated by exposure to light.
"The number of light and dark hours in a day might actually be a major environmental cue that's kind of driving circadian and circannual rhythms for lynx," says Lama, who notes that since climate change could make Maine warmer and rainier without affecting the amount of daylight, female lynx might end up having kittens "at times when conditions are actually suboptimal."
That's the kind of intriguing clue that wildlife conservation specialists can get from having complete genomes. While the price of sequencing all living creatures with a backbone may be upwards of $100 million, Jarvis thinks it would be worth it to "capture all endangered species, capture all vertebrates on the planet, and be a new model for how to do genomes."
AUDIE CORNISH, HOST:
If you count up all the different kinds of birds, mammals, fish, amphibians and reptiles, you get about 70,000 species. And an ambitious group of scientists wants to understand the full genetic makeup of every single one of them. Today, they unveiled the complete DNA sequences of 25 species, including the platypus and the zig-zag eel. NPR's Nell Greenfieldboyce reports they found some surprises.
NELL GREENFIELDBOYCE, BYLINE: The Vertebrate Genomes Project wants to get the genetic code of every known species with a backbone that's alive today; 71,657 named species. Erich Jarvis is a scientist at The Rockefeller University, who heads this effort. He says it should take about a decade and will ultimately cost something like $100 million.
ERICH JARVIS: One hundred million dollars is a lot of money. But if you can capture all endangered species, you know, capture all vertebrates on the planet and be, you know, a new model for how to do genomes, I think it's worth it.
GREENFIELDBOYCE: Over the last few years, the group has been refining their strategies and processes for taking a sample from an animal and figuring out its DNA code. Jarvis says they're now able to sequence six species a week and can get high-quality, complete results.
JARVIS: I think it's unconscionable to generate the lower draft quality genome sequences. It's a waste of money. It's a waste of time. You get decent science. You can, but you get lots of errors. You're missing lots of things.
GREENFIELDBOYCE: Take the zebra finch, for example; a songbird studied to help understand vocal learning in birds and people. It turns out these finches have seven more chromosomes than previously thought. Platypuses have eight more chromosomes. Each chromosome carries a ton of different genes.
JARVIS: People thought these genes were missing in birds and platypus, right? But they weren't missing. They just weren't sequenced with the older technologies.
GREENFIELDBOYCE: Their new technologies also avoid the opposite error - seeing extra genes that aren't actually there. Jarvis says it turns out this was a problem for tracing the evolution of the so-called love hormone oxytocin.
JARVIS: People in the past had incorrectly named additional genes of the oxytocin receptor in different fish and vertebrate lineages.
GREENFIELDBOYCE: The new reports in Nature and other scientific journals include the genetic code of wild species that are currently at risk, such as the kakapo, a critically endangered parrot in New Zealand.
Nell Greenfieldboyce, NPR News.
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