A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

By W. John Kress, David L. Erickson. PLoS ONE, 2007

1,424 citations recorded by the source corpus.

Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6eac400e4bbad4b22f15cf30191d88744cad3f20

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Citations in the corpus

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols (2011, background): “…the mitochondrial gene cox1, and the nuclear markers ITS, entire 18S (SSU) rRNA gene and 28S (LSU) rRNA gene (e.g. Bhadury et al. 2006; Fazekas et al. 2008; Hebert et al. 2004; Hollingsworth et al. 2009; Kress and Erickson 2007; Kress et al. 2005; Newmaster et al. 2008; Summerbell et al. 2005).”
Choosing and Using a Plant DNA Barcode (2011, methodology): “These were rpoC1+rpoB+matK or rpoC1+matK+trnH-psbA [6]; rbcL+trnH-psbA [7] and atpF-H+psbKI+matK (K.”
Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels (2012, methodology): “To test the design and resulting utility of PCR primers sequence-tagged using the helper program, we integrated the entire set (n = 164) of 10 nucleotide, edit distance five sequence tags (File S2) to primers amplifying the rbcLa locus in land plants [46,47].”
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants (2011, background): “Because none of the proposed barcodes perfectly meets all these criteria, it is generally considered necessary to use more than one marker to barcode plants (8, 10).”
Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species (2010, methodology): “In previous studies, most researchers accepted psbA-trnH as a potential plant barcode [9,15,16,18,19,21,33].”
DNA barcoding: a tool for improved taxon identification and detection of species diversity (2011, background): “The selection of plant barcode loci involved complex trade-offs between universality, sequence quality, species discrimination and cost (Kress et al. 2005; Chase et al. 2005, 2007; Kress and Erickson 2007; Erickson et al. 2008; Hollingsworth 2008; Lahaye et al. 2008, Ledford 2008; Hollingsworth et a”
Predicting tropical insect herbivore abundance from host plant traits and phylogeny (2012, methodology): “We sequenced according to published protocols (Kress et al. 2005, 2009, Kress and Erickson 2007), and all sequences were deposited in GenBank (accession numbers JF738369–JF739166; available online).6 We estimated phylogenetic relationships among all species of woody plants including trees, shrubs,…”
A DNA barcode for land plants (2009, background): “As reported elsewhere (7), trnH–psbA demonstrated good amplification across land plants with a single pair of primers (93% for angiosperms; Fig.”
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals (2010, neutral): “Many loci have been proposed as plant barcodes, including ITS [22,23], rbcL [24,25], psbA-trnH [24,26,27], and matK [26–28].”
DNA Barcoding to Detect Chilli Adulteration in Traded Black Pepper Powder (2014, background): “rbcL a-f rbcL a-r 5’ ATG TCA CCA CAA ACA GAG ACT AAA GC3’ 5’ GTA AAA TCA AGT CCA CCG CG 3’ Kress and Erickson, 2007 rpoC1–2 rpoC1–4 5’ GGC AAA GAG GGA AGA TTT CG3’ 5’ CCA TAA GCA TAT CTT GAG TTG G 3’ Ford et al., 2009 trnH-2 psbA-F 5’ CGC GCA TGG TGG ATT CAC AAT CC 3’ 5’ GTT ATG CAT GAA CGT AAT GCT…”
The Application of Biotechnology to Orchids (2013, methodology): “…spacer of the chloroplast genome are often used for molecular phylogenetic analysis of orchids (Table 1) (Hasebe et al., 1994; Hilu and Liang, 1997; Wilson, 2004; Kress and Erickson, 2007; Fazekas et al., 2008; Newmaster and Ragupathy, 2009; van den Berg et al., 2009; Parveen et al., 2012).”