Sunday, January 20, 2008

Plant genomes, animal genomes, more and more genomes!

I recently returned from the Plant and Animal Genome Conference (XVI, Jan. 12-16, in San Diego). This conference is much more applied than what I'm used to, but I came because it seemed a good place to see comparative genomics in full bloom, and that turned out to be true. I was struck by the extent to which the meeting was a showcase for vendors (Agilent, Sequenom, BioTrove, Illumina, Roche (now incorporating 454 and Nimblegen), Affymetrix, Applied Biosystems, Keygene, etc.), many of whom literally wined and dined conferees at their workshops.

However, I was also struck by the extent to which new high-throughput sequencing technologies are already in widespread use. Ronan O'Malley (Ecker lab) described the sequencing of Cvi, a strain of Arabidopsis distinct from the Columbia accession already determined; in the process he compared 454 and Solexa sequencing. Steve Jacobson (UCLA) described the repeated re-sequencing of (bisulfite-modified) Columbia for the purpose of studying cytosine methylation. Several more plant genomes are in in the pipeline, and a sense of the pace is conveyed by the fact that plenary speaker Eddy Rubin (JGI) "announced" the completion of the soybean genome almost in passing.

Other plenary talks were uniformly excellent. I missed the initial talk, by Jerry Caulder, which was apparently quite controversial. David Baulcombe referred to it by saying that the European perspective on genetically modified foods is different and that "by shying away from the hazards we don't gain credibility." Another notable aside was Michael Ashburner's statement that "there is no point in funding biomedical research unless you also fund informatics."