Phylogeny of Organisms Investigated by the Base-Pair Changes in the Stem Regions of Small and Large Ribosomal Subunit RNAs

Abstract

In order to obtain the evolutionary distance data that are as purely additive as possible, we have developed a novel method for evaluating the evolutionary distances from the base-pair changes in stem regions of ribosomal RNAs (rRNAs). The application of this method to small-subunit (SSU) and large-subunit (LSU) rRNAs provides the distance data, with which both the unweighted pair group method of analysis and the neighbor-joining method give almost the same tree topology of most organisms except for some Protoctista, thermophilic bacteria, parasitic organisms, and endosymbionts. Although the evolutionary distances calculated with LSU rRNAs are somewhat longer than those with SSU rRNAs, the difference, probably due to a slight difference in functional constraint, is substantially decreased when the distances are converted into the divergence times of organisms by the measure of the time scale estimated in each type of rRNAs. The divergence times of main branches agree fairly well with the geological record of organisms, at least after the appearance of oxygen-releasing photosynthesis, although the divergence times of Eukaryota, Archaebacteria, and Eubacteria are somewhat overestimated in comparison with the geological record of Earth formation. This result is explained by considering that the mutation rate is determined by the accumulation of misrepairs for DNA damage caused by radiation and that the effect of radiation had been stronger before the oxygen molecules became abundant in the atmosphere of the Earth.

Phylogenetic Relationship of Psychoactive Fungi Based on the rRNA Gene for a Large Subunit and Their Identification Using the TaqMan Assay

“…13,14) 2) The gene has stem and loop regions and nucleotide substitutions have occurred more frequently in the stem region than in the loop region. 15) This feature is very suitable to establish the species identification method using the TaqMan assay because the set of the fluorescence probe in the variable stem region and the primers in the conserved loop region enable us to construct the examination system covering various species. The LSU partial sequence was amplified by PCR using genomic DNA and directly sequenced.…”

Plant Pathogen Forensics: Capabilities, Needs, and Recommendations

“…While the error rates are likely fairly similar from one organism to another, the environments in which the organisms exist differ substantially as to how much damage their nucleic acid is likely to sustain from environmental stimuli (132). It is known that the mix of DNA repair systems differs among organisms.…”

The Influence of Selection on the Evolutionary Distance Estimated from the Base Changes Observed between Homologous Nucleotide Sequences

“…If the present formulation is reformed to analyse the base-pair changes observed in the stem regions of ribosomal RNAs and/or tRNAs, it widens the range of application to the organisms diverged at ten-fold further ancient times. As indicated in the previous papers (Otsuka et al, 1997b(Otsuka et al, , 1999, the change rate of stable base pairs of G : C, C : G, A : U and U : A is evaluated to be slower by one order of magnitude than the true mutation rate. These studies will be reported in the near future.…”