2024-03-29T13:20:21Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/110442018-08-01T10:02:54Zcom_10261_74com_10261_6col_10261_327
Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934
Subbotin, Sergei A.
Sturhan, Dieter
Vovlas, Nicola
Castillo, Pablo
Tambe, James Tanyi
Moens, Maurice
Baldwin, James G.
Character coding
Bayesian inference
D2–D3 expansion segments
Structural database
Helicotylenchus
Maximum parsimony
Rotylenchus
rRNA
Secondary structure model
Variability map
Knowledge of rRNA structure is increasingly important to assist phylogenetic analysis through reconstructing optimal alignment, utilizing molecule features as an additional source of data and refining appropriate models of evolution of the molecule. We describe a procedure of optimization for alignment and a new coding method for nucleotide sequence data using secondary structure models of the D2 and D3 expansion fragments of the LSU-rRNA gene reconstructed for fifteen nematode species of the agriculturally important and diverse family Hoplolaimidae, order Tylenchida. Using secondary structure information we converted the original sequence data into twenty-eight symbol codes and submitted the transformed data to maximum parsimony analysis. We also applied the original sequence data set for Bayesian inference. This used the doublet model with sixteen states of nucleotide doublets for the stem region and the standard model of DNA substitution with four nucleotide states for loops and bulges. By this approach, we demonstrate that using structural information for phylogenetic analyses led to trees with lower resolved relationships between clades and likely eliminated some artefactual support for misinterpreted relationships, such as paraphyly of Helicotylenchus or Rotylenchus. This study as well as future phylogenetic analyses is herein supported by the development of an on-line database, NEMrRNA, for rRNA molecules in a structural format for nematodes. We also have developed a new computer program, RNAstat, for calculation of nucleotide statistics designed and proposed for phylogenetic studies
Peer reviewed
2009-02-26T12:41:45Z
2009-02-26T12:41:45Z
2007-06-03
artículo
http://purl.org/coar/resource_type/c_6501
Molecular Phylogenetics and Evolution, 43: 881-890 (2007)
1055-7903
http://hdl.handle.net/10261/11044
10.1016/j.ympev.2006.09.019
en
http://dx.doi.org/10.1016/j.ympev.2006.09.019
none
553806 bytes
application/pdf
Elsevier