Singapore scientists join international study of 10,000 vertebrates' genomes

Agency for Science, Technology and Research (A*STAR), Singapore EurekAlert 4 Nov 09;

'Genomes contain information from the past -- they are molecular fossils,' said Nobel Laureate Sydney Brenner, M.D.

The Singapore laboratory that deciphered the DNA codes, or genomes, of the famed fugu (or pufferfish) and elephant shark, has joined The Genome 10K Project, an international effort to build an invaluable repository of DNA sequences on 10,000 species of animals for conducting comparative studies on a scale that currently can not be achieved.

Participating in The Genome 10K project, described in a paper published in the Nov. 5, 2009 issue of the Journal of Heredity, are 70 leading scientists at major zoos, museums, research centres and universities in North and South America, Europe, Australia as well as Asia. They will create a collection of tissue and DNA samples and then sequence and analyze the animals' genomes to reveal the complete genetic heritage of the 10,000 species.

The results will enable scientists worldwide to understand the genetic basis of adaptive changes that occur in vertebrates and predict how animals respond to climate change, pollution, emerging diseases and competition. In addition to aiding conservation efforts, this data will enable researchers to compare animal and human genomes, and reconstruct the evolutionary history of the human and other vertebrate genomes.

"The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved," said Nobel Laureate Sydney Brenner, M.D., who co-heads Singapore's Institute of Molecular and Cell Biology (IMCB) comparative genomics laboratory, which will participate in The Genome 10 K Project.

"Genomes contain information from the past – they are molecular fossils – and having sequences from vertebrates will be an essential source of rich information," added Dr. Brenner, who also is Scientific Advisor to the Chairman of Singapore's A*STAR (Agency for Science, Technology and Research), which oversees 14 biomedical sciences, and physical sciences and engineering research institutes, and seven consortia and centres at Biopolis and Fusionopolis, as well as their immediate vicinity.

One of the initiators of the Genome 10K project, David Haussler, Ph.D., Professor of Biomolecular Engineering at University of California, Santa Cruz, said, "For the first time, we have a chance to really see evolution in action, caught in the act of changing whole genomes. This is possible because the technology to sequence DNA is thousands of times more powerful now than it was just a decade ago, and is poised to get even more powerful very soon."

Byrappa Venkatesh, Ph.D., who heads IMCB's comparative genomics lab and is one of the chairpersons of the Genome 10K committee, said, "This project will not only generate sequences of all important vertebrate genomes that we were contemplating to sequence, but also will give us access to the latest sequencing technologies and sequence analysis tools for genomic studies in Singapore."

IMCB Executive Director Neal Copeland, Ph.D., added, "We are delighted and honored that IMCB is participating in this momentous project, which is a fine example of the international nature of science. Following the successful revelation of the fugu genome in 2002, IMCB is looking forward to making even more important contributions to the international field of genomics through the Genome 10K project and remains committed to using the tools of modern science to make important, basic discoveries that will advance the understanding of the human genome and diseases."

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In addition to Dr. Haussler, the project initiators are Stephen J. O'Brien, M.D., M.P.H., Chief of the Laboratory of Genomic Diversity at the National Cancer Institute and Oliver A. Ryder, Ph.D., Director of Genetics at the San Diego Zoo's Institute for Conservation Research and Adjunct Professor of Biology at UC San Diego.

For more information, please contact:
Wang Yunshi (Ms)
Corporate Communications
Agency for Science, Technology and Research (A*STAR)

Scientists Launch Effort To Sequence The DNA Of 10,000 Vertebrates
ScienceDaily 4 Nov 09;

Scientists have an ambitious new strategy for untangling the evolutionary history of humans and their biological relatives: Create a genetic menagerie made of the DNA of more than 10,000 vertebrate species. The plan, proposed by an international consortium of scientists, is to obtain, preserve, and sequence the DNA of approximately one species for each genus of living mammals, birds, reptiles, amphibians, and fish.

"Understanding the evolution of the vertebrates is one of the greatest detective stories in science," said David Haussler, a Howard Hughes Medical Institute investigator at the University of California, Santa Cruz (UCSC). "No one has ever really known how the elephant got its trunk, or how the leopard got its spots. This project will lay the foundation for work that will answer those questions and many others."

Known as the Genome 10K Project, the approximately $50 million initiative is "tremendously exciting science that will have great benefits for human and animal health," Haussler said. "Within our lifetimes, we could get a glimpse of the genetic changes that have given rise to some of the most diverse life forms on the planet."

Haussler is one of the lead authors of an article, published online November 5, 2009, in the Journal of Heredity, that outlines the project. The other lead authors include Stephen J. O'Brien, chief of the Laboratory of Genomic Diversity at the National Cancer Institute, and Oliver A. Ryder, director of genetics at the San Diego Zoo's Institute for Conservation Research and adjunct professor of biology at the University of California, San Diego. Coauthors and additional authors, who together make up a group called the Genome 10K Community of Scientists (G10KCOS), include geneticists, paleontologists, ecologists, conservationists, and other scientists representing major zoos, museums, research centers, and universities around the world.

The proposal originated at a meeting Haussler hosted at UCSC in April 2009. More than 50 scientists came together to discuss the merits of the project and its daunting logistic and financial challenges. "Some of the people at the meeting were initially skeptical," Haussler said. "But they quickly recognized the many advantages of a shared infrastructure and data analysis system."

The primary impetus behind the proposal is the rapidly expanding capability of DNA sequencers and the associated decline in sequencing costs. "We'll soon be in a situation where it will cost only a few thousand dollars to sequence a genome," Haussler said. "At that point, most of the cost will be getting samples, managing the project, and handling data."

All living vertebrates descend from a single marine species that lived 500-600 million years ago. Paleontologists do not know much about the physical appearance of that species, but because all of its descendents share certain characteristics, they know that it had segmented muscles, a forebrain, midbrain, and hind brain attached to spinal cord structures, and a sophisticated innate immune system.

That primitive vertebrate gave rise to what Haussler calls "one of the most spectacularly malleable branches of life." Vertebrates spread throughout the oceans, conquered land, and eventually took to the air. Over the course of time they produced stunning innovations, including multichambered hearts, bones and teeth, an internal skeleton that has supported the largest aquatic and terrestrial animals on the planet, and a species of primate -- Homo sapiens -- that has produced sophisticated language, culture, and technology.

By sequencing the DNA of 10,000 vertebrates -- roughly one-sixth of the 60,000 species estimated to be living today -- biologists will be able to reconstruct the genetic changes that gave rise to this astonishing diversity. Some parts of our DNA are very similar to the DNA of other vertebrates, reflecting our descent from a common ancestor, while other parts are markedly different. "We can understand the function of elements in the human genome by seeing what parts of the genome have changed and what parts have not changed in humans and other animals," said Haussler.

The project also will help conservation efforts by documenting the genomes and genetic diversity of threatened and endangered vertebrate species. By helping scientists predict how species will respond to climate change, pollution, emerging diseases, and invasive competitors, it will support the assessment, monitoring, and management of biological diversity.

The G10KCOS consortium has been developing guidelines for the collection, preservation, and documentation of cell lines and DNA samples. It also has been discussing potential public and private sources of funding for the project -- estimated at $50 million if the price of handling and sequencing each DNA sample eventually falls to $5,000. Said Haussler: "How do you raise $50 million? Ask nicely and make a strong case."

In planning the project, the G10KCOS group has used the Human Genome Project as a model. For example, the consortium plans to release sequencing data immediately according to standards developed for the sequencing of the human genome. Haussler also cited that project, which began before needed sequencing technologies were available, as evidence that it is worthwhile to begin planning for the Genome 10K Project before the cost of sequencing falls enough to make it feasible. "The time to start is now, or the job will get away from us," said Haussler. "The sequencing machines will be waiting, but the samples won't be ready."

Adapted from materials provided by Howard Hughes Medical Institute, via EurekAlert!, a service of AAAS.

10,000 species ... and the missing link
A*Star scientists to help collect DNA samples for worldwide project
Today Online 6 Nov 09;

SINGAPORE - How humans evolved could one day be scientifically reconstructed through a project involving scientists from Singapore's Agency for Science, Technology and Research (A*Star), who will help collect tissue and DNA samples from 10,000 species of animals.

Scientists from A*Star's Institute of Molecular and Cell Biology (IMCB) will team up with 70 leading scientists from major zoos, museums, research centres and universities in North and South America, Europe, Asia and Australia, in the effort called the Genome 10K Project.

Led by Professor Byrappa Venkatesh - who heads the Comparative Genomics Laboratory at IMCB and who is one of the chairpersons of the Genome 10K committee - the project will create an invaluable repository of DNA sequences for comparative studies on a scale never done before.

Taking Darwin's theory of evolution to another level, the project will allow scientists to reconstruct the evolutionary history of the human and other vertebrate genomes.

"Genomes contain information from the past - they are molecular fossils - and having sequences from vertebrates will be an essential source of rich information," said Nobel Laureate Dr Sydney Brenner, who is Scientific Adviser to the A*Star chairman and co-head of the IMCB laboratory.

"The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved," he added.

Aside from being able to compare animal and human genomes, scientists will also be able to understand the genetic changes and adaptations that occur in vertebrates.

This will help in conservation efforts, as scientists may be able to predict how animals respond to climate change, emerging diseases, and competition.

Said Prof Venkatesh: "This project will not only generate sequences of all important vertebrate genomes that we were contemplating to sequence, but also will give us access to the latest sequencing technologies and sequence analysis tools for genomic studies in Singapore."

The proposal for the project, launched in April this year, is outlined in a paper titled A proposal to obtain whole genome sequence for 10,000 vertebrate species, which will be published in the Journal of Heredity.

Evolution of man - Singapore joins first steps of gene study
Channel NewsAsia 5 Nov 09;

SINGAPORE: How humans evolved could one day be scientifically reconstucted through a project involving Singapore's A*STAR scientists, who will help collect tissue and DNA samples from 10,000 species of animals.

Scientists from A*STAR's Institute of Molecular and Cell Biology (IMCB) will team up with 70 leading scientists from major zoos, museums, research centres and universities in North and South America, Europe, Asia and Australia in the effort called the Genome 10K Project.

Led by Prof Byrappa Venkatesh, who heads the Comparative Genomics Laboratory at IMCB and who is one of the chairpersons of the Genome 10K committee, the project will create an invaluable repository of DNA sequences for comparative studies on a scale never done before.

Taking Darwin's theory of evolution to another level, the project will allow scientists to reconstruct the evolutionary history of the human and other vertebrate genomes.

"Genomes contain information from the past – they are molecular fossils – and having sequences from vertebrates will be an essential source of rich information," said Nobel Laureate Dr Sydney Brenner, who is the Scientific Advisor to A*STAR's Chairman and co-head of the IMCB laboratory.

"The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved," he added.

Aside from being able to compare animal and human genomes, scientists will also be able to understand the genetic changes and adaptions that occur in vertebrates.

This will help in conservation efforts as scientists may be able to predict how animals respond to climate change, emerging diseases, and competition.

Prof Venkatesh said, "This project will not only generate sequences of all important vertebrate genomes that we were contemplating to sequence, but also will give us access to the latest sequencing technologies and sequence analysis tools for genomic studies in Singapore."

The proposal for the project, launched in April 2009, is outlined in a paper entitled "A proposal to obtain whole genome sequence for 10,000 vertebrate species", which will be published in the Journal of Heredity.

The initiators of the Genome 10K Project include Prof David Haussler, Professor of Biomolecular Engineering at University of California, Santa Cruz; Dr Stephen J. O'Brien, Chief of the Laboratory of Genomic Diversity at the National Cancer Institute and Prof Oliver A. Ryder, Director of Genetics at the San Diego Zoo's Institute for Conservation Research and Adjunct Professor of Biology at UC San Diego.

- CNA/sf

Massive effort to decode DNA of 10,000 species
Research will also give insight into evolutionary history of humans
Amresh Gunasingham, Straits Times 7 Nov 09;

SCIENTISTS the world over are sequencing a veritable Noah's Ark, in the largest-ever project to trace the genetic history of humans.

Major zoos, museums and research centres, including the Agency for Science, Technology and Research's (A*Star) Institute of Molecular and Cell Biology (IMCB), are involved in the massive effort to decode the DNA of 10,000 animals, ranging from the tiger shark to the crocodile lizard.

In all, 68 scientists from five continents - North and South America, Europe, Asia and Australia - are working on what is called the Genome 10K Project.

There are about 60,000 known species of living vertebrates - creatures with backbones - broadly categorised into mammals, birds, reptiles, amphibians, fish and sharks.

So far, the genomes of 50 animals such as chickens and zebrafish have already been decoded. But by getting such information from one in six vertebrates on earth, the researchers hope to be able to compare them with the genetic make-up of humans, to reconstruct the evolutionary history of humans.

Said Dr Sydney Brenner, a Nobel laureate in physiology who co-heads the IMCB laboratory: 'The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved.

'Genomes contain information from the past - they are molecular fossils - and having sequences from vertebrates will be an essential source of rich information.'

The scientists hope to raise up to US$50 million (S$69 million) for the study, which was published in the Journal of Heredity on Thursday and is expected to take five years. The results will be freely available to researchers.

They also hope that by looking at the genetic changes in species as they adapt over time, they can better predict how vertebrates respond to climate change and pollution, to help in conservation efforts.

Said Professor David Haussler of the University of California, Santa Cruz, one of the three researchers to initiate the project: 'For the first time, we have a chance to really see evolution in action, caught in the act of changing whole genomes.'

Singapore's contribution is led by Professor Byrappa Venkatesh, who heads the Comparative Genomics Laboratory at IMCB, and chairs the committee that will oversee the sequencing and analysis of the 10,000 specimens.

'The idea is that once these genomes are sequenced, we can understand how they have evolved, how diverse they are, and how their biological identities have come about,' he explained.

Such detailed studies can, for example, boost efforts to conserve endangered species such as anteaters, the California condor and the Chinese sturgeon.

'Once we have sequenced these animals, we can look for adaptations, so we can see variations in populations and select mutations that are favourable. So, for example, when you want to breed these endangered species in captivity, you can select those that do not carry lethal mutations or genes,' he said.

Such a vast database will also boost efforts in understanding genetic diseases that afflict humans, he added.

'Sequencing the human genome has changed medicine, because we now can look to the root cause of genetic diseases and which genes cause them,' he explained.

Undertaking a project on such a large scale is possible only now because sequencing technology has become more affordable, he added, noting that when the human genome was sequenced in 2000, it cost around US$300 million per genome. This can be done now for US$50,000, and in a year or so, the cost is expected to shrink to US$5,000.

Scouring the world for promising fish is second nature to the 18-year veteran of the local research scene, and Singapore has proved to be an invaluable treasure trove of rare fish species., he said.

Fish make up nearly half of the living vertebrates alive today, and will comprise 4,000 out of the 10,000 used in the project.