An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

BMC Ecology and Evolution, June 2005

15932645

Céline Brochier, Patrick Forterre, Simonetta Gribaldo

The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets.