Evolution according to large ribosomal subunit RNA

Abstract

Evolutionary trees were constructed, by distance methods, from an alignment of 225 complete large subunit (LSU) rRNA sequences, representing Eucarya, Archaea, Bacteria, plastids, and mitochondria. A comparison was made with trees based on sets of small subunit (SSU) rRNA sequences. Trees constructed on the set of 172 species and organelles for which the sequences of both molecules are known had a very similar topology, at least with respect to the divergence order of large taxa such as the eukaryotic kingdoms and the bacterial divisions. However, since there are more than ten times as many SSU as LSU rRNA sequences, it is possible to select many SSU rRNA sequence sets of equivalent size but different species composition. The topologies of these trees showed considerable differences according to the particular species set selected. The effect of the dataset and of different distance correction methods on tree topology was tested for both LSU and SSU rRNA by repetitive random sampling of a single species from each large taxon. The impact of the species set on the topology of the resulting consensus trees is much lower using LSU than using SSU rRNA. This might imply that LSU rRNA is a better molecule for studying wide-range relationships. The mitochondria behave clearly as a monophyletic group, clustering with the Proteobacteria. Gram-positive bacteria appear as two distinct groups, which are found clustered together in very few cases. Archaea behave as if monophyletic in most cases, but with a low confidence.

What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram‐positive bacteria? A new proposal for the classification of prokaryotic organisms

“…While the phylogenies based on some gene sequences, namely Hsp70, GroEL (Hsp60) and sigma 70, show that these groups are distinct Viale et al, 1994;Gupta, 1995a;Gruber and Bryant, 1997;Gupta et al, 1997), in a number of other gene/protein phylogenies including those based on 16S RNA, these two groups are not resolved (Woese, 1987;1991;De Rijk et al, 1995;Eisen, 1995;Karlin et al, 1995;Baldauf et al, 1996). Hence, the question of whether the high-G þ C and the low-G þ C Gram-positive bacteria are phylogenetically distinct is presently unclear.…”

The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.

“…The most important factor in this selection is to choose molecules that are found ubiquitously in the living world, and SSU rRNA, large-subunit (LSU) rRNA (De Rijk et al, 1995;Ludwig et al, 1998), elongation factor EF-Tu/a (Ludwig et al, 1998), RNA polymerases (Klenk & Zillig, 1994), F 1 F 0 ATPase b-subunit (Ludwig et al, 1993(Ludwig et al, , 1998Ludwig & Schleifer, 1994), RecA protein (Wetmur et al, 1994;Eisen, 1995;Karlin et al, 1995) and Hsp60 heat-shock protein (Viale et al, 1994;Gupta, 1998) have, for this reason, proved to be good molecules for the phylogenetic inference of prokaryote taxonomy. SSU rRNA gene sequences have advantages over the other molecules.…”

Evaluating Putative Chimeric Sequences from PCR-Amplified Products

“…This procedure considers the variability specific to certain regions of the tested sequence type (i.e. rRNA gene sequences) since both conserved and variable regions are found in almost every known gene or DNA fragment and this is also the case for the rRNA genes (de Rijk et al, 1995).…”