NEW YORK, April 27 - Celera said Friday it had completed its final assembly of the mouse genome, and has now begun annotating the assembled genome.
Celera's assembly, which it achieved using its whole genome shotgun method, provides 6x coverage for the 129X1/SvJ, DBA/2J, and A/J strains of mouse. This follows Celera's February announcement that it had executed an initial 5.5x assembly of the mouse genome.
A public-private mouse sequencing consortium has also begun sequencing the the "black six" or C57BL6/J mouse, and was expected to announce earlier in the month that it had completed an initial draft sequence. But so far Celera's is the only mouse assembly to be publicly announced.
"We were able to do this so quickly and accurately because of our high-throughput DNA sequencing factory which has nearly 300 automated sequencers, proprietary algorithms, supercomputing power, and the whole genome shotgun technique," said Celera spokeswoman Heather Kowalski.
The mouse genome contains 2.6 billion base pairs, according to Celera, compared to the human genome's 2.9 billion base pairs. Celera has found almost 2.5 million SNPs among the three mouse strains. The company said earlier it would compile these SNPs into a database, but Kowalski said no plans for a database had been announced yet.
Craig Venter, Celera's chief scientific officer, said the assembly of the mouse genome provided further validation of Celera's controversial whole genome shotgun method.
Celera used this method, which involves randomly chopping up the genome into short segments of sequence, reading the sequence, then using computer algorithms to reconstruct this sequence, as one of its strategies for sequencing the human genome. The Human Genome Project initially rejected this approach, but moved to a modified BAC-based shotgun method later on. Celera's critics have said that it did not fully validate its whole genome shotgun approach in the human, because it used BAC clones from the public project to sequence its genome, as well as a genome map generated through the public effort.
In the mouse, however, Venter said "the sequence and assembly process was based entirely on Celera's proprietary data and bioinformatics expertise."
Meanwhile, the mouse sequencing consortium has adopted a variation of Celera's whole genome shotgun approach in its efforts
This consortium was formed in October 2000 to produce a publicly available mouse sequence in six months, and is funded by an alliance between Affymetrix, GlaxoSmithKline, the Merck Genome Research Institute, the US National Institutes of Health, and the Wellcome Trust. The sequencing is taking place at MIT's Whitehead Institute for Biomedical Research, Washington University School of Medicine in St. Louis, and the Sanger Center in the UK.
In February, the consortium said it would have 93 to 95 percent coverage by the beginning of April, and would construct a draft assembly over the course of the month. On March 27, Eric Lander, director of the Whitehead Institute's Center for Genome Research, said the consortium's mouse sequence would be complete within a couple of weeks.
As of Friday, the Consortium had not made any public reports as to its progress. Arthur Holden, chairman of the Mouse Consortium, declined to comment on Celera's announcement, but said the consortium would be releasing an official update within the next two weeks.