From Parakeet to Potoo, International Consortium Releases 100 High-Quality Vertebrate Genomes
Friday, August 30, 2019
UPDATE (October 2020): A preprint of the vaquita reference genome has been published.
With her distinctive dark eyeshadow, grey lipstick-like markings and delicate disposition, she was a natural film star. And her life certainly provided enough drama for any Hollywood blockbuster, complete with high-speed boat chases in pursuit of black market “cocaine of the sea” cartels. Unfortunately, her ending was not a happy one. But efforts by an international consortium of conservation geneticists are making sure her legacy isn’t lost.
The DNA of one of the last remaining vaquita porpoises in the world has been preserved and decoded, as part of an ambitious project to create chromosomal-level genome assemblies of all extant vertebrates species on Earth — 70,000 in total.
Members of the Vertebrate Genomes Project (VGP), an international consortium of more than 150 scientists from 50 academic, industry and government institutions in 12 countries, and the Earth Biogenome Project (EBP) gathered in New York on August 27 to announce the completion of the first 100 genomes, including several species of critical conservation and scientific interest. The assemblies represent 77 orders sequenced to such completeness for the first time, which, along with 13 from the previous data set, add to a total 90 of the 260 orders the group is seeking to sequence as Phase 1 of the project.
The most endangered among them is the vaquita. It is estimated that less than 20 remain in the world. The female whose sample contributed to the VGP effort died shortly after a rescue attempt by the group Vaquita CPR. It is hoped that her legacy will live on in the information extracted from her DNA; it has already provided insight into breeding patterns of the Phocoena sinus, whose habitat is limited to a small area in the northern Gulf of California.
“We hope and trust that useful information will result that may benefit other endangered species of threatened porpoises. And we are saddened to think that one day, these tissue samples may be all that is left of this animal,” said Oliver Ryder, Ph.D., director of Conservation Genetics for San Diego Zoo Global, where the vaquita’s tissue was taken to be stored in its Frozen Zoo repository.
Her plight was featured in a documentary film produced by Hollywood star Leonardo DiCaprio, Sea of Shadows, which follows the efforts of Mexican police forces to crack down on the vaquita’s biggest threat: illegal poaching of the totoaba fish (Totoaba macdonaldi), whose swim bladders, or maws, fetch high prices in Chinese markets for their use in traditional medicine. The tiny vaquita – the smallest member of the cetacean order that also includes whales, dolphins and other porpoises – gets trapped in the gillnets used by poachers.
Another species championed by DiCaprio, the Bolson tortoise (Gopherus flavomarginatus), also made the VGP sequencing list, as did two other critically endangered species (European eel and Smalltooth sawfish); seven endangered species (Blue whale, Grey crowned-crane, Green sea turtle, Atlantic halibut, Ring-tailed lemur, Chimpanzee and Golden aronawa); and eight vulnerable species (Sterlet, Thorny skate, Siamese fighting fish, Abyssinian ground hornbill, Atlantic cod, European turtle dove, Marmoset monkey and Red-bellied piranha).
Origin of a Species
Beyond conservation, the genomes of some of the species may also shed light on fundamental processes of evolution. Often referred to as ‘living dinosaurs’, leatherback sea turtles (Dermochelys coriacea) are an ancient lineage that possess unique physiological adaptations, including those that allow them to survive in cold waters exploiting habitats far beyond many other ectotherms.
“Their populations having declined by greater than 90%, Pacific leatherbacks are one of eight species among the most at risk of extinction in the near future protected by the United States NOAA under the Endangered Species Act,” said Lisa M. Komoroske, Assistant Professor of Conservation Genomics & Ecophysiology at the University of Massachusetts, Amherst.
She will be using the VGP genome to study the remaining genetic diversity in the species and to inform new leatherback conservation initiatives, including translocation across oceans to enable genetic mixing with other populations to avoid excessive inbreeding.
Weird and Wondrous
Among the species studied are a few truly unique – and strange – creatures.
The Great Potoo (aka Nyctibius grandis) may have a silly name and equally cartoonish look, with huge eyes and a ginormous mouth, but they’re no joke. They are generally heard rather than seen. During the day, they remain motionless in mimic of broken tree branches. At night, the nocturnal creatures make unsettling sounds that haunt the Neotropics, with mouths open wide to catch passing insects, occasionally moving to pounce on other prey in quick sallies.
Ubiquitous but Useful
Other genomes, like the chicken, may seem mundane, but could prove vital to agriculture and biomedical research.
The most commonly studied avian genome in these areas, the chicken genome is getting an important upgrade as part of the project. It is one of 12 genomes that reflects the DNA of both parents. Using a process called “trio binning”, the DNA of the parents are used to separate the DNA sequences of the child chromosomes to assemble two genomes (one each from mother and father) from one individual. Based on an assembly approach developed by Sergey Koren and Arang Rhie of the Adam Phillippy Lab at the National Human Genome Research Institute, these trio-based assemblies are 40-60% better than the non-trio based assemblies at separating out parentally-inherited DNA.
Approximately $600 million will be needed to complete the VGP project. Crowdsourcing among scientists has so far raised $4.8 million of the $6 million needed for Phase 1.
Get more information about the first 100 species.