Molecular Biology and Evolution, Vol 13, 150-169, Copyright © 1996 by Society for Molecular Biology and Evolution
RE Hickson, C Simon, A Cooper, GS Spicer, J Sullivan and D Penny
Secondary structure models are an important step for aligning sequences,
understanding probabilities of nucleotide substitutions, and evaluating the
reliability of phylogenetic reconstructions. A set of conserved sequence
motifs is derived from comparative sequence analysis of 184 invertebrate
and vertebrate taxa (including many taxa from the same genera, families,
and orders) with reference to a secondary structure model for domain III of
animal mitochondrial small subunit (12S) ribosomal RNA. A template is
presented to assist with secondary structure drawing. Our model is similar
to previous models but is more specific to mitochondrial DNA, fitting both
invertebrate and vertebrate groups, including taxa with markedly different
nucleotide compositions. The second half of the domain III sequence can be
difficult to align precisely, even when secondary structure information is
considered. This is especially true for comparisons of anciently diverged
taxa, but well-conserved motifs assist in determining biologically
meaningful alignments. Patterns of conservation and variability in both
paired and unpaired regions make differential phylogenetic weighting in
terms of "stems" and "loops" unsatisfactory. We emphasize looking carefully
at the sequence data before and during analyses, and advocate the use of
conserved motifs and other secondary structure information for assessing
sequencing fidelity.
ORIGINAL ARTICLE
Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA
School of Biological Sciences, Massey University.
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