A Stuttering Start to Plant DNA Barcoding: Microsatellites Present a Previously Overlooked Problem in Non-Coding Plastid Regions

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 bae calling. The downsream necessity of human intervention renders these non-coding regions sub-optimal for barcoding purposes.