title: A DNA mini-barcode for land plants.
abstract: Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).
authors.affiliation: Cullman Program for Molecular Systematics, The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA.
authors.forename: Damon P
authors.initials: DP
authors.lastname: Little
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000295:instrumentation / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D019669:Embryophyta / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*
chemical_list: D017931:DNA Primers; D018744:DNA, Plant
keywords: DNA barcoding; mini-barcode; rbcL