title: Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set.
abstract: The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group-specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species-rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species-rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Wenpan
authors.initials: W
authors.lastname: Dong
authors.forename: Tao
authors.initials: T
authors.lastname: Cheng
authors.forename: Changhao
authors.initials: C
authors.lastname: Li
authors.forename: Chao
authors.initials: C
authors.lastname: Xu
authors.forename: Ping
authors.initials: P
authors.lastname: Long
authors.forename: Chumming
authors.initials: C
authors.lastname: Chen
authors.forename: Shiliang
authors.initials: S
authors.lastname: Zhou
mesh_terms: D019295:Computational Biology; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods*; D010944:Plants / Q000145:classification* / Q000235:genetics*; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics*
chemical_list: D017931:DNA Primers; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase
keywords: DNA barcode; nucleotide diversity; rbcLb; universal primers