A large team of researchers, including a computer scientist at Washington University in St. Louis, has effectively completed the genome sequence of the common laboratory brown rat, Rattus norvegicus, This makes the third mammal to be sequenced, following the human and mouse.
The Rat Genome Sequencing Project Consortium (RGSPC), led by the Human Genome Sequencing Center at Baylor College of Medicine (BCM-HGSC) in Houston, in conjunction with the National Heart, Lung and Blood Institute (NHLBI) and the National Human Genome Research Institute (NHGRI), announced today the generation and analysis of the genome sequence of the Brown Norway (BN) rat. The high quality ‘draft’ sequence covers over 90 percent of the genome. The primary results are presented in the April 1 issue of Nature, and an additional thirty manuscripts describing further detailed analyses are contained in the April issue of Genome Research.
“This is an investment that is destined to yield major payoffs in the fight against human disease,” said NIH Director Elias A. Zerhouni, M.D. “For nearly 200 years, the laboratory rat has played a valuable role in efforts to understand human biology and to develop new and better drugs. Now, armed with this sequencing data, a new generation of researchers will be able to greatly improve the utility of rat models and thereby improve human health.”
The laboratory rat is an indispensable tool in experimental medicine and drug development and has made inestimable contributions to human health. The new data expand and consolidate its role as a research resource. The BN rat sequence is the third complete mammalian genome to be sequenced to high quality and described in a major scientific publication. Three-way comparisons with the human and mouse genomes will help to resolve details of mammalian evolution.
“The sequencing of the rat genome constitutes another major milestone in our effort to expand our knowledge of the human genome,” said NHGRI Director Francis S. Collins, M.D., Ph.D. “As we build upon the foundation laid by the Human Genome Project, it’s become clear that comparing the human genome with those of other organisms is the most powerful tool available to understand the complex genomic components involved in human health and disease.”
Michael R. Brent, Ph.D., associate professor of computer science and engineering at Washington University in St. Louis, contributed to the analysis of the gene set. According to Brent, results from the study show that the change from the last common ancestor of rodents and humans has occurred much faster along the rodent branch than change along the human branch. Also, the study finds that approximately one-fourth of the human genome is shared with both rats and mice.
That’s approximately 825 shared, non-repetitive megabases of DNA by all three animals.
“It’s surprising that the amount of shared DNA is so small,” Brent said.
Relative to their last common ancestor, the rodent lineage has mutated more than the human lineage, Brent pointed out, while analysis of the human genome reveals significantly more segmental duplication – a biological process whereby a large piece of the genome is copied in small numbers. Segmental duplications are one of the key things that differentiate the human genome from that of chimpanzees, and may contribute to the physical and behavioral difference between the two species.
Rodent mutation is due to various different factors, an obvious one being generation time – they reproduce faster than humans. The results of the analysis show that the rat has mutated slightly more frequently than the mouse from the last common ancestor.
“It’s not clear how to explain that because they both have the same generation time,” Brent said.
Results also show there is nearly two times more mutation in the brown rat male germ line than the female germ line, perhaps because there are more cell divisions along the path to making a sperm than the path to making an egg, and thus more chance for error Females carry two X chromosomes and males one. The study finds less mutation in the X chromosome than in chromosomes equally divided between males and females.
A network of centers generated data and resources for the RGSP, including the BCM-HGSC, Celera Genomics, Genome Therapeutics Corporation, British Columbia Cancer Agency Genome Sciences Centre, The Institute for Genomic Research, University of Utah, Medical College of Wisconsin, The Children’s Hospital of Oakland Research Institute, and Max-Delbrück-Center for Molecular Medicine (Berlin). After assembly of the genome at the BCM-HGSC, analysis was performed by an international team, representing over 20 groups in six countries and relying largely on gene and protein predictions produced by the Ensembl project of the EMBL-EBI and Sanger Institute (UK). Funding for the RGSP was largely provided by the NHLBI and the NHGRI with additional private funding provided to the BCM-HGSC by the Kleberg Foundation.
The study found the rat genome contains similar numbers of genes to the human and mouse genomes but at 2.75 gigabases (Gb) is smaller than human (2.9 Gb) and slightly larger than mouse (2.6 Gb). Almost all human genes known to be associated with diseases have counterparts in the rat genome and appear highly conserved through mammalian evolution. A selected few families of genes have been expanded in the rat, including smell receptors and genes for dealing with toxins, and these give clues to the distinctive physiology of the species.
Current examples of use of the rat in human medical research include surgery, transplantation, cancer, diabetes, psychiatric disorders including behavioral intervention and addiction, neural regeneration, wound and bone healing, space motion sickness, and cardiovascular disease. In drug development, the rat is routinely employed both to demonstrate therapeutic efficacy and assess toxicity of novel therapeutic compounds prior to human clinical trials. The genome sequence will facilitate all of these studies.
As the third mammalian genome to be completely sequenced, comparison of the rat genome to human and mouse allows a unique view of mammalian evolution. The rat data shows about 40 percent of the modern mammalian genome derives from the last common mammalian ancestor. These ‘core’ one billion bases encode nearly all the genes and their regulatory signals, accounting for the similarities among mammals. These parts of the genome will be of particular focus in other mammals as new genomes are explored, and the events leading to the current species are unraveled.
“Future work aimed at identifying the genomic differences that contribute to evolution and disease will benefit from analyses such as these, which will become increasingly powerful as the repertoire of mammalian genome sequences expands” said Richard Gibbs, Ph.D., director of the BCM-HGSC and overall principal investigator of the RGSP.
To ensure a high quality draft, the combined approach used both whole genome shotgun (WGS) and BAC clone sequencing techniques. To merge these into the final draft sequence, the BCM-HGSC developed the Atlas software package for genome assembly. The resulting genome sequence was contained in 291 large segments, with a typical length of 19 megabases (Mb). Moreover, the structure of the 3 percent of the genome containing recent duplications, where genes are born, was accurately determined by the Atlas assembler. These statistics match or exceed other draft genome sequences. Overall, the combined approach takes advantage of strengths of previous methods, either pure WGS or pure BAC sequencing, with few of the disadvantages.
“The issue of efficacy of WGS versus other approaches to the sequencing of large genomes remains a matter of earnest scientific debate, and methodology for producing draft sequences continues to evolve” said Dr. George Weinstock, co-director of the BCM-HGSC.
Following the rat project, the BCM-HGSC has undertaken the genomes of the honeybee and sea urchin, and is now working on the Bovine and Rhesus macaque projects. Like the rat, each will lead to a high quality genome draft sequence. With advances in genome technologies it is likely that genomes from many different species can be analyzed in the next three years.