A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea)

Joseph J. Gillespie, James B. Munro, John M. Heraty, Matthew J. Yoder, Albert K. Owen, Andrew E. Carmichael

Research output: Contribution to journalArticle

Abstract

We analyze the secondary structure of two expansion segments (D2, D3) of the 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are composed of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction or regions of slipped-strand compensation. Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phytogeny reconstruction in these and closely related apocritan taxa.

Original languageEnglish (US)
Pages (from-to)1593-1608
Number of pages16
JournalMolecular biology and evolution
Volume22
Issue number7
DOIs
StatePublished - Jul 1 2005
Externally publishedYes

Fingerprint

Wasps
Hymenoptera
Structural Models
wasp
Base Pairing
ribosomal RNA
Sequence Alignment
Hydrogen Bonding
rRNA Genes
secondary structure
Sequence Analysis
hydrogen bonding
homology
Nucleotides
sequence alignment
sequence analysis
nucleotides
contraction
hydrogen
genes

Keywords

  • 28S
  • Chalcidoid
  • Expansion segment
  • Homology
  • Multiple sequence alignment
  • Ribosome
  • Secondary structure
  • rRNA

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera : Chalcidoidea). / Gillespie, Joseph J.; Munro, James B.; Heraty, John M.; Yoder, Matthew J.; Owen, Albert K.; Carmichael, Andrew E.

In: Molecular biology and evolution, Vol. 22, No. 7, 01.07.2005, p. 1593-1608.

Research output: Contribution to journalArticle

Gillespie, Joseph J. ; Munro, James B. ; Heraty, John M. ; Yoder, Matthew J. ; Owen, Albert K. ; Carmichael, Andrew E. / A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera : Chalcidoidea). In: Molecular biology and evolution. 2005 ; Vol. 22, No. 7. pp. 1593-1608.
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