DNA sequencing at the genome level may clarify evolutionary trees based on individual gene sequences--or muddy the waters further. "In the literature there's been a debate as to whether Thermotoga is the deepest branch of the Eubacteria or the second deepest (after Aquifex). But Aquifex, recently sequenced, looked more like E. coli than an archaean," says Venter. The Aquifex work3 compared 848 genes to those of E. coli and the archaean Methanococcus jannaschii. Despite greater overall genetic proximity to E. coli, Aquifex does share some genes of unknown function with the archaean.
The genome of Thermotoga echoes archaean input both in number of corresponding genes, and, perhaps more tellingly, in their organization. "A quarter of the genes are most similar to Archaea! This ... was very clear. The next best matches were far away," declares Claire Fraser, president of TIGR. Of the 1,877 protein-encoding genes among the 1,860,725-base-pair genome, 451 ...
