DNA Barcoding in Plants: Past, Present, and Future

Abstract

AbstractDNA barcoding is a method of identifying biological specimens and assigning them to their respective species. It involves sequencing of single/multiple short stretch/stretches of previously agreed-upon genomic region which evolves fast enough to allow species-level discrimination. Thus, obtained sequence(s) of unknown samples serve as a molecular identifier which is compared to a reference database of museum samples using specialized algorithms to reveal the identity of the specimen under study. In effect it complements classical taxonomy to quickly identify any newly obtained sample and aid in describing, naming, and classifying it to species. Unlike in animals where DNA barcoding is well standardized utilizing mitochondrial gene CO1, DNA barcoding in plants has perpetually been a matter of concern due to low substitution rates of plant mitochondrial genome. Alternatively, plastid genome has been targeted in case of plants for DNA barcoding purpose with some amount of success but ambiguities remain regarding selection of barcode region that can provide best possible resolution. A large number of studies tested the efficiency of seven leading candidate plastid DNA regions (matK, rbcL, rpoB, rpoC1 genes and atpF–atpH, psbK–psbI, trnH–psbA spacers) as the standard DNA barcode for plants. Based on universality, sequence quality, and species discrimination rate, a double-locus barcode (rbcL+ matK) system is suggested to perform best in plants. However, internal transcribed spacer (ITS) region of plastid gene ycf1 has recently been suggested as the most promising single-locus plant DNA barcode. On contrary, a recent study argues that with an ever-growing sequence database even double-locus barcode (rbcL+ matK) system might become unfit for precise discrimination purpose. Hence, with the availability of next-generation sequencing technologies, partial genome representation-based barcoding, genome skimming based barcoding, full-length multi-barcoding (FLMB), etc. might be the preferred approaches to improve diagnostic power. DNA barcoding in plants not only speeds up writing the encyclopedia of life, but also opens up the possibility of establishing Digital Plant Identification System (DPIS) which works independent of type, age, or developmental stage of the sample under study. Hence, if used properly, DNA barcoding can be an effective and efficient tool for exploring and protecting biodiversity, expedite bioprospecting, and defending against bio-piracy.KeywordsDNA BarcodingITS matK Species identification