title: Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.
abstract: A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
authors.forename: Lian-Ming
authors.initials: LM
authors.lastname: Gao
authors.forename: Hong-Tao
authors.initials: HT
authors.lastname: Li
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: Xue-Jun
authors.initials: XJ
authors.lastname: Ge
authors.forename: Jian-Quan
authors.initials: JQ
authors.lastname: Liu
authors.forename: Zhi-Duan
authors.initials: ZD
authors.lastname: Chen
authors.forename: Shi-Liang
authors.initials: SL
authors.lastname: Zhou
authors.forename: Shi-Lin
authors.initials: SL
authors.lastname: Chen
authors.forename: Jun-Bo
authors.initials: JB
authors.lastname: Yang
authors.forename: Cheng-Xin
authors.initials: CX
authors.lastname: Fu
authors.forename: Chun-Xia
authors.initials: CX
authors.lastname: Zeng
authors.forename: Hai-Fei
authors.initials: HF
authors.lastname: Yan
authors.forename: Ying-Jie
authors.initials: YJ
authors.lastname: Zhu
authors.forename: Yong-Shuai
authors.initials: YS
authors.lastname: Sun
authors.forename: Si-Yun
authors.initials: SY
authors.lastname: Chen
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.forename: Kun
authors.initials: K
authors.lastname: Wang
authors.forename: Tuo
authors.initials: T
authors.lastname: Yang
authors.forename: Guang-Wen
authors.initials: GW
authors.lastname: Duan
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D032462:Cycadopsida / Q000145:classification / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018742:DNA, Chloroplast / Q000145:classification / Q000235:genetics; D021901:DNA, Intergenic / Q000145:classification / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D030541:Databases, Genetic / Q000706:statistics & numerical data; D004722:Endoribonucleases / Q000145:classification / Q000235:genetics; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D009713:Nucleotidyltransferases / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D015203:Reproducibility of Results; D012273:Ribulose-Bisphosphate Carboxylase / Q000145:classification / Q000235:genetics; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast; D021901:DNA, Intergenic; D021903:DNA, Ribosomal Spacer; D010940:Plant Proteins; D009713:Nucleotidyltransferases; C034038:mRNA maturase; D004722:Endoribonucleases; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase
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