Chase, Mark W. , Devey, Dion , Clarkson, James J. , Cowan, Robyn .
Non-coding plastid DNA and DNA barcoding: a critical evaluation.
Non-coding plastid DNA regions (introns, intergenic spacers) have been proposed as potential DNA barcoding markers for general use in the land plants because they are expected to exhibit higher rates of divergence than coding regions. Based a set of 96 pairs of closely related species spread across the seed plants, we assessed performance of two non-coding plastid regions, psbA-trnH and atpF-H intergenic spacers, that have been proposed as barcode markers and compared these to several coding regions. Rates of sequence divergence are indeed somewhat higher than for coding regions that have been proposed, such as plastid matK, but not more than 1.5 times more variable. We also took a critical look at the frequency of occurrence of plastid microsatellite regions in these two non-coding regions and found that for our 96 pairs of taxa, 32% and 52% of taxa for psbA-trnH and atpF-H, respectively, had serious problems with “stutter”, such that one or both strands did not produce clean sequences that could be handled successfully in an automated format, such as is currently in operation for cox1 sequencing in several groups of animals. Such high rates of occurrence of plastid microsatellite regions pose serious problems for the standardized use of plastid non-coding regions as plant barcoding makers. To be an effective marker, complete full-length sequences must be able to be produced for both strands of the proposed markers, but this expectation cannot be met for non-coding regions, making them unacceptable candidates in a standardized protocol for DNA barcoding of land plants.
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1 - Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey, TW9 3AB, United Kingdom
DNA Bar coding
Presentation Type: Oral Paper:Papers for Topics
Date: Monday, July 28th, 2008
Time: 3:45 PM