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Extinct Species Genome Sequencing Effort Gets €2M Boost

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NEW YORK (GenomeWeb) – Researchers at the University of Copenhagen have been awarded €2 million ($2.3 million) to examine the possibility of using next-generation sequencing to reconstruct the genomes of ancient and extinct species.

The project, called "Exploring and exploiting the potential of extinct genome sequencing," has been funded through Horizon 2020, the European Framework Programme for Research and Innovation. The effort commenced last month and will run through March 2021.

Thomas Gilbert, a professor of paleogenomics at the University of Copenhagen, said his group previously had looked at samples from extinct species but had only focused on sequencing mitochondrial DNA. Gilbert's lab had also developed laboratory and data analysis methods for generating whole genomes from ancient samples using Illumina HiSeq 4000 instruments.

The point of the new grant, he told GenomeWeb, is to combine the two approaches.

"We know that mtDNA as a single marker gives very limited insights into such processes, so as the technology is there now, it's the obvious extra step," Gilbert said.

Gilbert's team also aims to "explore the realities of de-extinction," meaning the ability to both sequence the genomes of extinct species, and to perhaps even bring such species back to life. De-extinction efforts related to the woolly mammoth have received attention in recent years, with some researchers imagining a theme park of de-extinct animals.

Gilbert said that he has no such plans to revive an extinct species, and acknowledged that there has been a lot of "hype" around de-extinction. In the grant abstract, he called such hopes "naïve," and said that they don't account for the financial and technical challenges that face them. The new project therefore is meant in part to explore the limits of such genome reconstruction. Toward that goal, the group will develop new laboratory and bioinformatic methods with a focus on reducing costs while improving the quality of genome reconstruction from poor-quality DNA.

"I aim to build a scientifically grounded framework against which the possibilities and limitations of extinct genome reconstruction can be assessed," said Gilbert. "How complete would the ancient genomes that we could actually reconstruct be?" asked Gilbert. "What would we not be able to reconstruct? What does this mean about the hypothetical recreated species we'd end up with? How dodo-like would a reconstructed dodo bird be?"

While the bulk of the team's work will focus on assessing the best protocols and technologies to achieve such aims, Gilbert said it does intend to work with samples from ancient and extinct species, including investigating "population crashes and genomic consequences" on black and white rhinoceroses and crested ibis, as well as sequencing the genome of the Christmas Island rat, which was last sighted over a hundred years ago. Other candidate species for the new project include the woolly rhinoceros, great auk, and saber-toothed cats.

All of the work will be carried out within the Center for GeoGenetics, which is part of the Natural History Museum of Denmark and overseen by the university. Gilbert's group at the center has spent years working on techniques for analyzing ancient DNA. In December, they published an evaluation of using single-stranded versus double-stranded DNA library preparation for ancient DNA samples. Also last year, the group published in BMC Bioinformatics a new method that uses phasing algorithms to reconstruct both source and inserted organelle sequences, information that they claimed could be of use in evolutionary and comparative genomic studies.

While Gilbert's immediate setup for the project is the Illumina HiSeq 4000, he said that the group will adopt new technologies as they become available. He noted that the DNA fragments from extinct species tend to be short, so the longer reads of platforms such as those from 10X Genomics or Pacific Biosciences are at this time unnecessary. He declined to further address his group's methods.

The main challenge facing Gilbert's team is how to best reconstruct the genomes of extinct species when DNA fragments are on average between 40 and 50 base pairs. "Is there any scope for de novo genomes, or are we only limited to mapping to extant reference genomes?" asked Gilbert. "How does evolutionary divergence affect how well we can do that? Are there ways to improve it?" Gilbert and his team hope to answer these questions in the next five years.

Gilbert said he hopes the methods he develops will be useful for other paleogenomics researchers who are working with challenging samples.

"Once it's below 30 base pair fragments, it's largely useless," said Gilbert. "This has a million-year window, although temperature dependent, so we can't do much about that," he said. "But if in my project we can improve the quality of the reconstructed ancient genomes, then that should be of benefit to anyone who wants to exploit such material."

Love Dalén, a professor of evolutionary genetics at the Swedish Museum of Natural History in Stockholm, welcomed the new project, calling it "novel and ambitious."

Dalén, who is not involved with the project, told GenomeWeb that Gilbert's work is "important, both from a fundamental scientific perspective to develop a better understanding of species' evolutionary histories, and also for applied genome editing and de-extinction projects."

He also noted that Gilbert's team will apply paleogenomic methods to investigate the processes that take place as species move towards the brink of extinction. "This will provide essential information on how genetic diversity is lost as species decline in population size and become fragmented into small isolated populations," said Dalén. "Such information will be very helpful in assessing the future extinction risk in endangered species."

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