title: Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants.
abstract: We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that 'false' species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.
authors.affiliation: Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK.
authors.forename: Mike J
authors.initials: MJ
authors.lastname: Wilkinson
authors.affiliation: School of Computer Science, The University of Adelaide, SA 5005, Australia.
authors.forename: Claudia
authors.initials: C
authors.lastname: Szabo
authors.affiliation: Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK.
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Ford
authors.affiliation: School of Computer Science, The University of Adelaide, SA 5005, Australia.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Yarom
authors.affiliation: School of Agriculture, Food and Wine, Waite Campus, The University of Adelaide, SA 5064, Australia.
authors.forename: Adam E
authors.initials: AE
authors.lastname: Croxford
authors.affiliation: School of Animal &Veterinary Sciences, Roseworthy Campus, The University of Adelaide, SA 5371, Australia.
authors.forename: Amanda
authors.initials: A
authors.lastname: Camp
authors.affiliation: Australian Genome Research Facility, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Gooding
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D012015:Reference Standards; D013010:Sonication; D013045:Species Specificity
chemical_list: D018744:DNA, Plant