I Dream of Genome

It is an exciting time to be a geneticist, in large part because, with the advent of the era of genome sequencing, we stand to see an explosion of information that will advance our understanding of biology.

When I consider the amazing progress that has been made through the Human Genome Project, I think, Pinch me, am I dreaming? I am actively involved with Genome10K, with the goal to obtain the complete genome sequences of 10,000 vertebrate species in the next 5-10 years.

Genome sequences of animals from the San Diego Zoo and San Diego Zoo Safari Park have already been produced, allowing more detailed insights into the biology of the African savannah elephant, western lowland gorilla, Bornean and Sumatran orangutans, South African ostrich and Peré David deer. Availability of the genomes of these species (and related geneses) sets the stage for studies of their ecology, risk of disease, and population history.

The recent decrease in the cost of genome sequencing makes such an ambitious task a feasible proposition. What may prove more challenging to my colleagues, David Haussler (U.C. Santa Cruz) and Stephen O’Brien, head of an Institute in St. Petersburg, Russia, and myself is having the right samples from such a diversity of species.

Fortunately, the assets of banked tissues and cell cultures of the Frozen Zoo® are contributing to the development of a new era of biological investigation. We are engaged in an effort that Genome10K advocate, Harris Lewin, U.C. Davis Vice Chancellor of Research, has suggested is “among the most significant experiments in the history of biology.”

The Genome10K Community of Scientists has come together and pledged the sample resources needed for the sequencing effort encompassing fishes, amphibians, reptiles, birds and mammals. Scientific partnerships with genome sequencing centers in several countries have helped launch this amazing effort.  The world’s largest genome center, BGI, in Shenzhen, China has already completed sequencing and assembling the genomes of 48 vertebrate species, with 32 in progress, and 26 proposed, but not yet started.

The value of having diverse genome sequences available to conservation scientists bolsters multiple areas, including animal health, population management, identifying historic patterns of animal dispersals and migrations, and detecting genetic changes accompanying species diversification and adaptation to varying environments.

A fundamental goal of species conservation efforts involves preservation of the gene pool of a species. This gene pool encompasses the genetic variation of a species and constitutes its genetic capital. It provides the basis for resilience to changing environmental conditions, and represents the source of variation that allows species to diversify and continue the evolutionary process.

Increasingly, the description of gene pool diversity will be at the level of changes in single bases of DNA across the genomes of individuals. Thus, Genome10K is providing the framework for the future of conservation genetic studies and applications. 

For example, forensic studies to identify individuals and their place of origin can be more precise and powerful using genomic information. The identification of the genetic basis of invasiveness in plants may contribute to detecting and controlling invasive plants, and managing the deterioration of habitats that threatens many species.

At the other end of the spectrum, genome sequencing technology is being adapted to allow more rapid, informative and cost effective evaluation of the diets of animals through DNA analysis of their feces.

It is an exciting time for geneticists and for anyone interested in following the developments of a thrilling scientific field as it grows and contributes knowledge to assist in wildlife conservation efforts.

By Oliver Ryder, Ph.D., Director of Genetics