Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well

By A. Fazekas, K. Burgess, Prasad R. Kesanakurti, S. Graham, Steven G. Newmaster, B. Husband, Diana M. Percy, Mehrdad Hajibabaei, S. Barrett. PLoS ONE, 2008

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A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF–atpH, and psbK–psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85–100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK–psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69–71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b8b5659166653224d4a8e63ed2e8ff8518b756f4

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Citations in the corpus

Evaluation of 10 plant barcodes in Bryophyta (Mosses) (2010, background): “Primer universality and ease of amplification and sequencing are crucial characteristics for each candidate barcode, beyond the power of species discrimination (Chase et al., 2007; Fazekas et al., 2008).”
Choosing and Using a Plant DNA Barcode (2011, background): “[3] who noted ‘‘regardless of the region(s) ultimately adopted for plant barcoding, there will always be some species that would be better resolved by some other region’’.”
Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode (2011, methodology): “%) of the samples were from a previously published barcoding study collected during the same time period (Fazekas et al. 2008).”
The Application of Biotechnology to Orchids (2013, methodology): “matK and rbcL, the plastid trnL intron, the trnL-F spacer as well as the trnH-psbA intergenic 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., 2”
Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing (2013, background): “…USDA-ARS, Chatsworth, NJ, USA N. Vorsa Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, USA E. Gillespie Department of Biology, Marshall University, Huntington, WV, USA K. Kron Department of Biology, Wake Forest University, Winston-Salem, NC, USA”
Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols (2011, background): “…rRNA gene, 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…”
Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species (2010, background): “In previous studies, most researchers accepted psbA-trnH as a potential plant barcode [9,15,16,18,19,21,33].”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, background): “Several research groups have proposed different plastid regions/combinations as their preferred barcodes, but no consensus has emerged (e.g. Pennisi, 2007; Erickson et al., 2008; Fazekas et al., 2008; Hollingsworth et al., 2009; Kress et al., 2009).”
New universal matK primers for DNA barcoding angiosperms (2011, methodology): “However, difficulties were often encountered when the available primers were used (Sass et al., 2007; Fazekas et al., 2008).”