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Comparative Chloroplast Genomics

Wolf, Paul G. [1], Duff, R. Joel [2].

RNA editing in land plant organellar genomes and its effect on phylogenetic analysis.

Although DNA sequences from plant genomes are often of direct utility to evolutionary biologists, the plants themselves sometimes modify the information prior to use. In violation of the central dogma of molecular genetics, some organisms edit the RNA after transcription (prior to protein synthesis) so that the mRNA used is not complementary to the original genomic sequence. This process, known as RNA editing, can only be documented by evaluating the transcript, e.g., via cDNA sequencing. Here we describe the nature of RNA editing in plant organellar genomes, we present hypotheses on why such a mechanism might have evolved, and we show how RNA editing can have unwanted effects on phylogenetic analyses. RNA editing is probably accomplished by enzymes that evolved for some other cellular process, perhaps to protect cells from invading nucleic acids. The presence of RNA editing enzymes either releases selective constraints on genomic sequences or even results in selection for a nonsense sequence. The result, for protein-coding genes, is a genomic sequence that would produce a non-functional protein were it not for RNA editing. RNA editing sites are distributed across mitochondrial and chloroplast genes and it appears that these sites can be switched on and off in different lineages. Thus, inclusion of RNA editing sites in phylogenetic analysis of genomic sequences can confound inferences. However, removal of such sites can cause loss of phylogenetic signal. Although RNA editing appears to be relatively rare in seed plants, it is very common (up to 10% of nucleotides) in other land plant clades. Strategies for evaluating and minimizing the effects of RNA editing on phylogenetic analyses will be discussed.


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1 - Utah State University, Department of Biology, College of Science, 5305 Old Main Hill, Logan, Utah, 84322, USA
2 - University of Akron, Department of Biology, Akron, Ohio, 44320-3908, USA

Keywords:
cDNA
transcript
RNA
hornwort.

Presentation Type: Symposium or Colloquium Presentation
Session: 19-2
Location: Salon K - Austin Grand Ballroom/Hilton
Date: Monday, August 15th, 2005
Time: 2:30 PM
Abstract ID:279


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