Cinnamon (the Cat), Genome Decoded

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Tony Rook
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Cinnamon (the Cat), Genome Decoded

Here is a recent Associated Press Release written by AP Science Writer Malcolm Ritter

Scientists decode most of Mo. cat's DNA
Wed Oct 31, 2007

NEW YORK - An Abyssinian cat from Missouri, named Cinnamon, has just made scientific history. Researchers have largely decoded her DNA, a step that may aid the search for treatments for both feline and human diseases.

The report adds cats to the roughly two dozen mammals whose DNA has been unraveled, a list that includes dogs, chimps, rats, mice, cows and of course, people.

Why add cats? They get more than 200 diseases that resemble human illnesses, and knowing the details of their genetic makeup should help in the search for vaccines and treatments, researchers say. The list includes a cat version of AIDS, SARS, diabetes, retinal disease and spina bifida, said Stephen J. O'Brien of the National Cancer Institute.

The new work is reported in the November issue of the journal Genome Research by a team including O'Brien and colleague Joan Pontius. It covers about two-thirds of the DNA of Cinnamon, a research cat that lives at the University of Missouri in Columbia; more complete results are expected next year, O'Brien said.

Richard Gibbs of the Baylor College of Medicine in Houston, who led a team that decoded the DNA of a monkey called the rhesus macaque, called the new work "a good outline" of cat DNA. Scientists are looking forward to the complete version, which will be useful for making detailed comparisons to the DNA of other animals, he said.

The full complement of an organism's DNA is called its genome. In cats, as in people, it's made up of nearly 3 billion building blocks. The sequence of those blocks spells out the hereditary information, just as strings of letters spell out sentences. Decoding a genome, which is called sequencing, means identifying the order of the building blocks.

The new work identified 20,285 genes in the cat, probably about 95 percent of the animal's full complement, O'Brien said. That's similar to the 20,000-25,000 genes estimated for humans.

Original Link Reference -

Associated Press Release

Tony Rook
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And here is the Genome

And here is the Genome Research Press Release....

Domestic cat genome sequenced

A report that appears in the scientific journal Genome Research (www.genome.org) details the first assembly, annotation, and comparative analysis of the domestic cat genome (Felis catus).

The DNA of a 4-year-old Abyssinian cat named Cinnamon, whose well-documented lineage can be traced back several generations to Sweden, has been sequenced. Cinnamon is one of several mammals that are currently being analyzed using light (two-fold) genome sequence coverage. To make sense of Cinnamons raw sequence data, a multi-center collaboration of scientists leveraged information from previously sequenced mammalian genomes as well as previous gene-mapping studies in the cat. In doing so, they found that Cinnamons sequences spanned about 65% of the euchromatic (gene-containing) regions of the feline genome.

The similarity between the cat genome and six recently completed mammalian genomes (human, chimpanzee, mouse, rat, dog, and cow) allowed the scientists to identify 20,285 putative genes in the cat genome. The comparison also revealed hundreds of chromosomal rearrangements that have occurred among the different lineages of mammals since they diverged from a diminutive ancestor that roamed the earth among the dinosaurs some 100 million years ago.

The genome sequence analysis is certainly expected to lead to health benefits for domestic cats, 90 million of which are owned by Americans alone, according to The Humane Society. But the domestic cat also serves as an excellent model for human disease, which is one reason why the National Human Genome Research Institute (NHGRI) initially authorized the cat genome sequencing project three years ago.

Domestic cats possess over 250 naturally occurring hereditary disorders, many of which are similar to genetic pathologies in humans. For example, Cinnamons pedigree carries a genetic mutation that causes retinitis pigmentosa, a degenerative eye disease that can lead to blindness. In humans, retinitis pigmentosa affects 1 in 3,500 Americans. The domestic cat also serves as an excellent model for human infectious diseases, including HIV/AIDS. Feline immunodeficiency virus (FIV) is a genetic relative of human immunodeficiency virus (HIV), which causes AIDS.

Using the cat genome sequence data, the researchers identified several hundred thousand genomic variants (known as SNPs, DIPs, and STRs), which can be used to determine the genetic basis for common hereditary diseases. The scientists have already used these variants to identify the causative gene for Cinnamons retinitis pigmentosa (they published a paper describing this study in the May/June, 2007 issue of the Journal of Heredity). These variants will also be useful for parentage testing, forensic analysis, and studies of evolution, including the reconstruction of domestication processes, fancy breed development, and ecological adaptation among the great roaring cats.

The researchers also analyzed the feline genome for interesting features such as microRNAs, Numts (pronounced new mightsnuclear genomic fragments that migrated to cat chromosomes from mitochondria), and a vast sea of selfish DNA-like repetitive elements. The repetitive elements included scores of genomic stretches from historic retroviruses, some with known links to cancer.

The Cat Genome Project is based at the National Cancer Institute (Frederick, Md.). Cinnamon lives in a cat colony maintained at the University of Missouri-Columbia. The sequencing data were generated by Agencourt Bioscience Corporation (Beverly, Mass.). Funding for the project was supported in part by the Intramural Research Program of NIH, National Cancer Institute, Center for Cancer Research, and in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract N01-CO-12400.

# # #

Media contacts:
Drs. Stephen J. OBrien, Joan U. Pontius, and Marilyn Raymond, who are co-authors on the Genome Research article, are available for comment through the National Cancer Institutes Office of Media Relations (e-mail: eval(unescape('%64%6f%63%75%6d%65%6e%74%2e%77%72%69%74%65%28%27%3c%61%20%68%72%65%66%3d%22%6d%61%69%6c%74%6f%3a%6e%63%69%70%72%65%73%73%6f%66%66%69%63%65%72%73%40%6d%61%69%6c%2e%6e%69%68%2e%67%6f%76%22%3e%6e%63%69%70%72%65%73%73%6f%66%66%69%63%65%72%73%40%6d%61%69%6c%2e%6e%69%68%2e%67%6f%76%3c%2f%61%3e%27%29%3b')); phone: 301-496-6641).

Original Link Reference:

Genome Research Press Release

Tony Rook
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And here is the citation to

And here is the citation to the original article appearing in Genome Research...

Pontius, J.U., Mullikin, J.C., Smith, D., Agencourt Sequencing Team, Lindblad-Toh, K., Gnerre, S., Clamp, M., Chang, J., Stephens, R., Neelam, B., Volfovsky, N., Schffer, A.A., Agarwala, R., Narfstrm, K., Murphy, W.J., Giger, U., Roca, A.L., Antunes, A., Menotti-Raymond, M., Yuhki, N., Pecon-Slattery, J., Johnson, W.E., Bourque, G., Tesler, G., NISC Comparative Sequencing Program, OBrien, S.J. 2007. Initial sequence and comparative analysis of the cat genome. Genome Res. 17: 1675-1689. [doi:10.1101/gr.6380007]

To read the full text article link to
Genome Research and look for the Nov 2007 issue.