Authors: Seongho Ryu Yoonkyung Do David H A Fitch Won Kim Bud Mishra
Publish Date: 2008/03/25
Volume: 66, Issue: 4, Pages: 368-383
Abstract
Subrepeats within the ribosomal gene rDNA intergenic spacer IGS play an important role in enhancing RNA polymerase I transcription Despite this functional role and presumed selective constraint there is surprisingly little sequence similarity among IGS subrepeats of different species This sequence dissimilarity corresponds with the fast insertiondeletion indel rates observed in short mononucleotide microsatellites here referred to as polyN runs where N is any nucleotide which are relatively abundant in rDNA IGS subrepeats Some species have different types of IGS subrepeats that share speciesspecific polyN run patterns This finding indicates that many IGS subrepeats within species share a common evolutionary history Furthermore by aligning sequences after modifying them by the dropout method ie by disregarding polyN runs during the sequence aligning step we sought to uncover evolutionarily shared similarities that fail to be recognized by current alignment programs To ensure that the improved similarities in the computed alignments are not a chance artifact we calibrated and corrected the IGS subrepeat sequences for the influence of repeat length and estimated the statistical significance of the alignments in terms of a stringent pvalue obtained by the dropout method by comparing them to null models constructed using random sequence sets from the same genomes We found that most diverse kinds of rDNA IGS subrepeats in one species must have been derived from a common ancestral subrepeat and that it is possible to infer the evolutionary relationships among the IGS subrepeats of different species by comparative genomics methods based on dropout alignments
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