Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation

We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw...

Full description

Saved in:
Bibliographic Details
Published in:Journal of molecular evolution 2005-07, Vol.61 (1), p.114-137
Main Authors: Gillespie, Joseph J, Yoder, Matthew J, Wharton, Robert A
Format: Article
Language:English
Subjects:
Animals
Apocrita
Base Pairing
Base Sequence
Bayes Theorem
Bioinformatics
Braconidae
Evolution
Hymenoptera
Hymenoptera - classification
Hymenoptera - genetics
Ichneumonidae
Ichneumonoidea
Insecta
Models, Genetic
Molecular Sequence Data
Nucleic Acid Conformation
Phylogeny
Protein Structure, Secondary
RNA, Ribosomal, 18S - genetics
RNA, Ribosomal, 28S - genetics
Sequence Alignment
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.
ISSN:0022-2844
1432-1432
DOI:10.1007/s00239-004-0246-x