A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions

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Abstract:

Plastid microsatellites are simple mono/dinucleotide repeats that can cause in-vitro taq polymerase errors leading to 'stutter' peaks that reduce the clarity and reliability of electropherograms. As an efficient and automated barcoding protocol requires high-quality raw data, this paper investigates the suitability of the psbA-trnH and atpF-H regions of the plastid genome for automated barcoding purposes. Amplification of 92 individuals from species pairs and triplets was undertaken. Of these, 59% of atpF-H species samples and 36% of psbA-trnH species samples showed evidence of microsatellite-induced errors in electropherogram base calling. The downstream necessity of human intervention renders these non-coding regions sub-optimal for barcoding purposes.

Keywords: ATPF-H; AUTOMATED-BARCODING; DNA MICROSATELLITES; ELECTROPHEROGRAMS; NON-CODING PLASTID DNA; PSBA-TRNH

Document Type: Research Article

Affiliations: Molecular Systematics Section, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW93DS, U.K.

Publication date: February 1, 2009

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