Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers

Seongho Ryu, Yoonkyung Do, David H A Fitch, Won Kim, Bud Mishra

Research output: Contribution to journalArticle

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 insertion-deletion (indel) rates observed in short mononucleotide microsatellites (here referred to as poly[N] runs, where N is any nucleotide), which are relatively abundant in rDNA IGS subrepeats. Some species have different types of IGS subrepeats that share species-specific poly(N) 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, i.e., by disregarding poly(N) 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 p-value) 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.

Original languageEnglish (US)
Pages (from-to)368-383
Number of pages16
JournalJournal of Molecular Evolution
Volume66
Issue number4
DOIs
StatePublished - Apr 2008

Fingerprint

dropouts
Ribosomal DNA
intergenic DNA
homology
RNA Polymerase I
Genes
Genomics
Microsatellite Repeats
Artifacts
Transcription
Nucleotides
History
Genome
functional role
artifact
analysis
alignment
RNA
genomics
DNA-directed RNA polymerase

Keywords

  • Comparative genomics
  • Dropout alignment method
  • Homopolymeric runs
  • Intergenic spacer
  • Mononucleotide microsatellites
  • Poly(N)
  • Ribosomal DNA
  • Subrepeat

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers. / Ryu, Seongho; Do, Yoonkyung; Fitch, David H A; Kim, Won; Mishra, Bud.

In: Journal of Molecular Evolution, Vol. 66, No. 4, 04.2008, p. 368-383.

Research output: Contribution to journalArticle

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