Archaeal Phylogeny Based on Ribosomal Proteins

Abstract

Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in most of the archaeal species. This phylogeny was remarkably congruent with the rRNA phylogeny, suggesting that both reflected the actual phylogeny of the domain Archaea even if some nodes remained unresolved. In both cases, the branches leading to hyperthermophilic species were short, suggesting that the evolutionary rate of their genes has been slowed down by structural constraints related to environmental adaptation. In addition, to estimate the impact of lateral gene transfer (LGT) on our tree reconstruction, we used a new method that revealed that 8 genes out of the 53 ribosomal proteins used in our study were likely affected by LGT. This strongly suggested that a core of 45 nontransferred ribosomal protein genes existed in Archaea that can be tentatively used to infer the phylogeny of this domain. Interestingly, the tree obtained using only the eight ribosomal proteins likely affected by LGT was not very different from the consensus tree, indicating that LGT mainly brought random phylogenetic noise. The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity.

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

“…In contrast with the genes of bacterial origin in thaumarchaeotal fosmids, these ORFs concentrate in the region downstream the 16S rDNAs (Figure 1). The opposite region is occupied in all group II fosmids by the large spectinomycin operon of ribosomal proteins, which are know to be reluctant to HGT (Matte-Tailliez et al, 2002) or recombination events that might disrupt the operon organisation. Therefore, the presence of this large operon is likely responsible for the lack of observable HGT events in this genomic region.…”

Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

“…A likely explanation for the conflicting placements of these bacterial strains and species is the acquisition of different gene copies. Since the strains were isolated from different individuals of the same host species, and transfer events are believed to be influenced more by physical proximity of strains than by phylogenetic relatedness (Matte-Tailliez et al, 2002;Toth et al, 2006), it is possible that the bacterial strains acquired their copies of the genes from neighbouring bacteria on the same plant.…”

The role of archaea in the origin of eukaryotes

“…с изучения эвриархей и кренархей с использованием 16S рРНК в качестве консервативного филогенетиче-ского маркера [8]. В последующие годы был применен более широкий спектр маркеров, в том числе наборы рибосомных белков [9], осуществлено полногеномное секвенирование, использованы новые методы и модели филогенетического анализа, включая сетевые техноло-гии. Различия в топологических схемах, разработанных разными авторами, зависят от выбранного методическо-го подхода.…”