The premise is that a function as critical as protein synthesis would not have changed much over evolutionary time. The Aquifex work 3 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. The runner-up so far is Aquifex , with 18 percent of the coding sequences similar to those of Archaea.
Genomes harbor subtleties of sequence.
These genes are in clusters where their order is identical in Thermotoga and the archaea. Plus, eight clusters have a specific pattern of alternating repeated and unique sequences seen also in Methanococcus jannaschii and Archaeoglobus fulgidus , the only two archaeans sequenced so far. If pre-cells promiscuously swapped cassettes of genes, deciphering how cells arose may be extremely challenging. But not everyone agrees that detecting gene cassettes today necessarily reflects gene movement so long ago. It could be normal vertical inheritance, or it could be horizontal transfer from an indeterminate source.