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Venter & Fraser Publish 1.5X Sequence Coverage of Their Poodle

NEW YORK, Sept. 25 (GenomeWeb News) - Researchers at The Institute for Genomic Research and The Center for the Advancement of Genomics have sequenced and analyzed the dog genome, the groups said today.


According to TIGR and TCAG, the research, which appears in the Sept. 26 issue of Science -- and is one of Craig Venter's and Claire Fraser's pet poodles -- shows that partial shotgun sequencing is a "cost-effective and efficient" way of sequencing and analyzing "many more large eukaryotic genomes" against which reference genomes exist.


The researchers assembled 6.22 million sequences of canine DNA for 1.5X coverage, or 78 percent, of the genome. Comparing the sequence data with existing drafts of the human and mouse sequences, the teams found that the canine lineage was the first to diverge from the common ancestor of the three species, and that the human and dog "are much more similar to each other at the genetic level than to the mouse."


The canine genome is 2.4 billion base pairs long and has 78 chromosomes, which are "considerably reshuffled" when compared against Carnivora, the most recent common ancestral mammalian order in which dogs reside, according to Stephen O'Brien and William Murphy, who wrote an accompanying editorial to the sequence paper. Both men are researchers at the Laboratory of Genomic Diversity at the National Cancer Institute.


The TIGR and TCAG teams assembled the whole genome shotgun sequence of 6.22 million reads into 1.9 million contigs and 850,000 singletons, which were tied into 522,101 scaffolds. Them researchers also identified 974,400 SNPs in the canine genome and found that more than 25 percent of the genome, or roughly 650 million base pairs, overlap the human sequence.


The researchers also used the data to identify an equivalent canine gene for 75 percent of the known human genes. Specifically, the teams found 18,473 canine orthologs of the 24,567 annotated human genes. The sequence data "has revealed several hundred gene families that have expanded or contracted since divergence of the dog lineage from our common ancestor," TIGR and TCAG said in a statement. "For example," the groups went on, "the dog genome is predicted to encode a much greater diversity of olfactory receptors than we find in human."

"In little more than a decade genomics has advanced greatly and we now have approximately 150 completed genomes, including the human, mouse and fruit fly, in the public domain," Craig Venter, president of TCAG and the J. Craig Venter Science Foundation, which paid for the dog genome research, said in the statement. "Our new method is an efficient and effective way of sequencing that will allow more organisms to be analyzed while still providing significant information."

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