Meeting Highlights: Plant, Animal and Microbe Genomes X

Francis Collins (NIH, USA) started the first plenary session with a talk entitled Large-scale sequencing: Past, Present and Future. He recounted the history of the human genome project. The project will achieve all of the goals set out by the NRC panel in 1988, in spring 2003. They will have 99% coverage of the euchromatin, no centromeres, and a small number of gaps, due to uncloneable regions (they are working on new technologies to overcome this problem). Observations that came from the draft sequence include that we have only 30–40 000 genes, that the male mutation rate is twice that of females and that ‘junk DNA’ contains remnants of the raw materials of evolution. He prefers to say that we are in the ‘genome era’ rather than the ‘post-genome era’, as we don’t know everything about the genome yet. The next phase of HGP will involve medical, comparative and functional genomics, and proteomics. He feels that their main investment is most likely to be in the technologies required for these approaches, as none of the existing ones are good enough to allow scale-up yet. The mouse genome is being sequenced using a combination of whole genome shotgun and cloneby-clone BAC approach, and is going to be finished to a high level. He thinks it is unlikely that this level of finishing will be done for another mammalian genome. The Trans NIH BAC sequencing effort, which includes a BAC construction project, is a key sign of this change in emphasis. These projects cover all animals, fungi and eukaryote protists. He also highlighted a call by NHGRI for white papers proposing organisms for genome sequencing (other than eubacteria, archaea and plants). He expects that 5–10 years of vigorous activity in large-scale sequencing should cover most important organisms. Then, he said, we will be in the ‘post-sequencing era’! Paul Keim (Northern Arizona University, USA) gave a presentation on Anthrax, which he described as a very poor pathogen, with a very good toxin. The ability of its spore form to stay viable in the soil for long periods of time prompted its selection as a biological weapon in the USA, UK and Russia. Global collections of bacterial isolates show very low variation, which could be because it is recently evolved, or because it evolves very slowly, which could be caused by the spore stage. TIGR have almost completed the sequence of the 5.5 Mb chromosome and the two plasmids of B. anthracis and are moving onto other isolates. His group have been identifying the regions with the most variation, which are the tandem repeats. They use PCR with flanking primers to fingerprint strains, testing a huge number of loci per colony. Of the 55 VNTR loci they use, the 8 most hypervariable regions are population markers. In 1000 genotyped isolates, they have seen just over 200 unique genotypes. In the phylogenetic tree they see a major type (A) found in North America, the UK and Turkey, the animal vaccine strain clusters with this group. The B group are predominantly from South Africa and there is also a very rare B2 group. In the US they see a correlation of anthrax presence with cattle trails, which they believe may be the original route of spread. Michael Bevan (JIC, UK) spoke about the Arabidopsis genome and comparisons to other plant genomes. The genome was finished at the end of 2000; about 60% of the predicted genes had similarity to genes of known function and were assigned putative functions. Arabidopsis has more Comparative and Functional Genomics Comp Funct Genom 2002; 3: 178–193. Published online 14 March 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002 /cfg.168