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Vermin Close In On Mankind: Rodent Genomes Near the Finish Line

BOSTON, Oct. 4-They may be unpopular among ordinary Bostonians, but vermin were the superstars of this morning's session of the Genome Sequencing and Analysis Conference.

Talks by the Whitehead Institute's Kerstin Lindblad-Toh and by Baylor Genome Sequencing Center's Richard Gibbs showed that genome projects for both the rat and the mouse are making rapid progress-and may pack some surprises about human genetics to boot.


For one thing, analysis of the mouse genome has downgraded the forecast for gene totals in both man and mouse. The mouse may have only 26,000 to 27,000 genes, Lindblad-Toh said, which suggests that the human gene count will be in the same range-in any case, well under the 30,000 mark.


Further facts about the mouse: thanks to DNA deletions, its genome comes in around 2.5 Gb, significantly smaller than the 2.9 Gb human genome. It may be smaller, but it's also faster, apparently evolving at about twice the rate.


The mouse team, including researchers from the Sanger Institute, WashingtonUniversity,and other institutes, has finished 7.7-fold whole genome shotgun coverage and assembly, and is now working on BAC-based coverage, Lindblad-Toh said. The work is currently under review for publication.


They expect to finish the mouse sequence in 2005.


In other rodent news: Gibbs said flatly that his consortium "has sequenced the rat." The group, including researchers from Celera, Genome Therapeutics, Baylor, The Institute for Genomic Research, and the Universityof Utah, has reached about the same fold coverage as the mouse. The "official release of Rat One" will come in mid-November, he said, adding: "It's in excellent shape."


This project, which began later than the mouse sequencing effort, sped through its sequencing thanks to a hybrid approach that combines BAC by BAC assembly with whole genome shotgun sequencing, said Gibbs. The group has already deposited about 17,500 "enriched BACs" in GenBank, and assembled these into BAC contigs (Gibbs' term is "BACtigs") that now cover 2.3 Gb of the predicted 2.5-2.6 Gb of the rat genome.


With its success in conquering the rat genome, the combined approach "is very substantially proven," said Gibbs.

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