Ribosomal ITS sequences and plant phylogenetic inference.

@article{lvarez2003RibosomalIS,
  title={Ribosomal ITS sequences and plant phylogenetic inference.},
  author={In{\'e}s {\'A}lvarez and Jonathan F. Wendel},
  journal={Molecular phylogenetics and evolution},
  year={2003},
  volume={29 3},
  pages={
          417-34
        }
}
One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. [...] Key Result These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction.Expand
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  • Nucleic acids research
  • 2007
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References

SHOWING 1-10 OF 219 REFERENCES
Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of Ribosomal DNA in Winteraceae
The internal transcribed spacers and the 5.8S coding region of nuclear ribosomal DNA were sequenced and analyzed to address questions of generic relationships in Winteraceae. The molecular dataExpand
Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus.
TLDR
The hypothesis that the contrasting phylogenetic histories drawn from Quercus using ITS data are not strictly related to technical differences between laboratories, but that they have rather been generated from the analysis of paralogous sequences, best reconciles the available data. Expand
Ribosomal DNA: Molecular Evolution and Phylogenetic Inference
TLDR
An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. Expand
A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence.
TLDR
It is argued that the morphological data set contains poor phylogenetic signal and advocate simultaneous analysis of the three data sets (total evidence approach) so that morphological characters are tested for homology by congruence with molecular data. Expand
Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL
TLDR
Two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups indicate that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Expand
Phylogenetic Relationships of Geum (Rosaceae) and Relatives Inferred from the nrITS and trnL-trnF Regions
TLDR
Morphological characters, notably fruit characters, mapped onto the combined tree show patterns of widespread parallel evolution and reversals—or possibly the effects of reticulations. Expand
Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae.
  • B. G. Baldwin
  • Biology, Medicine
  • Molecular phylogenetics and evolution
  • 1992
TLDR
Findings indicate that the internal transcribed spacer region in plants should be further explored as a promising source of nuclear phylogenetic markers. Expand
Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA
TLDR
The results from Krigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Expand
Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
TLDR
The nuclear small-subunit rDNA sequences (16S-like) evolve rela­ tively slowly and are useful for studying distantly related organisms, whereas the mitochondrial rRNA genes evolve more rapidly and can be useful at the ordinal or family level. Expand
L. A. S. JOHNSON REVIEW No. 2 Use of nuclear genes for phylogeny reconstruction in plants
TLDR
Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Expand
...
1
2
3
4
5
...