'Genomic zoo' plan unveiled

 

AN INTERNATIONAL team of scientists has embarked on one of the most ambitious research projects yet attempted in evolutionary biology. They plan to map the genomes of 10,000 vertebrate animals including fish, birds, reptiles, amphibians and mammals, and in the process create a “genomic zoo”, writes DICK AHLSTROM

Ireland will be at the centre of this research, given the involvement of Dr Emma Teeling of University College Dublin. The study will provide “an unprecedented view of vertebrate evolution,” she says. “We are going to understand how vertebrate life evolved. We will learn how their genomes changed in response to environmental challenges.”

Details of how the Genome 10K Project will conduct its business are published this morning in the online research publication, Journal of Heredity. Its three lead authors, David Haussler, Stephen J O’Brien and Oliver A Ryder, are behind the hugely complex undertaking.

They called a three-day meeting at the University of California, Santa Cruz, last April, for initial discussions, and since then they have built up a group of 68 scientists from around the world, including Teeling.

Her involvement is not surprising, given that her work on comparative studies of bat genomes is known around the world. She lectures in evolutionary biology in UCD’s school of biological and environmental science and runs what is known on campus as the “BatLab”.

She was also involved in collaborative research work with Genome 10Kproposer Stephen J O’Brien, who is chief of the laboratory of genomic diversity at the US National Cancer Institute.

Teeling was in awe of the enormity of the undertaking. “It is a very ambitious project. What we are trying to do is gather together tissues from labs from all around the world including mammals, fish and birds, to try and sequence the genomes from 10,000 species.”

Powerful computers will then allow these genomes to be contrasted and compared, providing an unprecedented understanding of the evolution of genes and how these vary between species.

For example, immune systems could be compared to see the differences and similarities as the organism responded to the challenges presented by life. “How they survived is written in their genes,” she says.

“For the first time, we have a chance to really see evolution in action, caught in the act of changing whole genomes,” UC Santa Cruz’s Prof Haussler said yesterday. “Analysis of this data will be a far greater challenge than anything yet attempted in comparative genomics.” Co-author of the Journal paper and Nobel laureate, Prof Sydney Brenner, said of the value of the project. “Genomes contain information from the past – they are molecular fossils – and having sequences from vertebrates, will be an essential source of rich information.”

It is not simply a matter of collecting samples and then sequencing their DNA, Teeling points out. The human genome was sequenced over a decade and at a cost of more than $1,000 million (€636m). The latest systems can now do this in months for between $50,000 (€34,111) and $100,000 (€68,222).

“What we want to be able to do is sequence a genome for $1,000,” Teeling says. “We are moving into completely new territory.”

It will mean encouraging the development of the next generation of sequencing technology. “This is going to be the push to move the technology forward, just like the human genome project was the push that moved the earlier technology forward,” she says.

Meanwhile a huge logistics effort is under way. “Right now we are gathering the genomes together. We also have to develop the technology and also raise money,” Teeling says.

The plan is to establish 20 centres around the world where DNA sequencing can be undertaken. All of the researchers are anxious that Genome 10K is recognised as a worldwide effort and not dependent on a single centre or country.

This also means that Ireland could aspire to be one of the 20 sequencing centres, Teeling says. Ireland already has a solid reputation for the quality of its bioinformatics expertise, the computer skills that will enable genomes to be analysed and compared.