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

Abstract

AbstractPlastid 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.