Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode

Abstract

Summary 1.A major goal of DNA barcoding is to identify species in local floras and ecological communities. With the consensus of a two-locus DNA barcode (rbcL+matK) by the Consortium for the Barcode of Life (CBOL) Plant Working Group (2009), barcoding efforts have begun to focus on building the barcode library for land plants.2. Here, we establish a barcoding database for a temperate flora of moderate taxonomic breadth at the Koffler Scientific Reserve, Ontario, Canada based on the rbcL+matK barcode. We evaluated the performance of this combination in comparison with three other potential supplementary regions (the coding region rpoC1 and two non-coding intergenic spacers trnH-psbA and atpF-atpH). We examined these markers singly and in combination to evaluate their discriminatory power among 436 species in 269 genera of land plants. 3. Using high-throughput techniques, we recovered a high-quality sequence from at least one region for 98.2% of the 513 samples screened; 55% had complete coverage across all five gene regions. Sequencing success was highest for rbcL (91.4% of samples collected) and lowest for rpoC1 (74.5%). The two coding regions rbcL and matK provided a relatively high number of high-quality bi-directional sequences compared with the non-coding intergenic spacers, and in combination were able to correctly identify 93.1% of the species sampled. Marginal increases in species resolution were obtained with the inclusion of the trnH-psbA intergenic spacer (95.3%), or by using all five gene regions combined (97.3%). 4. There was a weak relation between the number of species per genus and identification success rate using rbcL+matK; 100% for monotypic genera (70.5% of the flora) and 83.6% for polytypic genera. Identification success using the rbcL+matK barcode was higher (100%) for gymnosperms, bryophytes, lycophytes and monilophytes (collectively representing 5% of the flora), compared with angiosperms (92.7%). 5. Our results indicate that the rbcL+matK barcode can provide an acceptably high rate of species resolution in the context of this and other local northern temperate floras. It does so in a cost-effective manner, with relatively modest laboratory effort, and despite the presence of missing data from individual plastid regions in a subset of samples.

Testing the utility of matK and ITS DNA regions for discrimination of Allium species

“…In this way, an unknown plant accession can be assigned to a species by comparing the nucleotide sequences of the barcode DNA region (Hebert et al, 2003;Stoeckle, 2003;Kress and Erikson, 2008;Pang et al, 2011). In addition, the DNA region for barcoding should be highly recoverable, should have a high percentage of species resolution, and should be cost-effective (Burgess et al, 2011). In this study, utility of the nucleotide sequences of matK was tested as a DNA barcode for discrimination of the Allium species and was compared with the previously suggested ITS region.…”

“…In this respect, nucleotide sequences of matK, rpoC1 rpoB, trnH-PsbA rbcL, atpF-atpH, and psbK-psbI and their combinations were recently tested for barcoding plant species by the Consortium for the Barcode of Life (CBOL) Plant Working Group (Hollingsworth et al, 2009) and matK and rbcL were accepted as a 2-locus DNA barcode. The matK DNA region has been tested for discrimination of many plant species as a single barcode region or in combination with other proposed plant barcode sequences in recent studies (Lahaye et al, 2008;Burgess et al, 2011;De Mattia et al, 2011;Du et al, 2011;Gu et al 2011;Guo et al, 2011;Li et al, 2011;Pang et al, 2011;Seberg et al, 2012;Bandara et al, 2013). matK as a barcode DNA has advantages of effective species discrimination power, high quality sequence recovery, easy experimental procedures and sequence alignment, and lack of allelic polymorphisms or multiple paralogous copies compared to nuclear DNA regions (Lahaye et al, 2008;Hollingsworth et al, 2009;Burgess et al, 2011).…”

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

“…rpoB and rpoC1 for Resedaceae ; rbcL ? matK for flora of South central Ontario, Canada (Burgess et al 2011), and rbcL ? matK ?…”

DNA barcoding of arid wild plants using rbcL gene sequences

“…Some ecologists have started using the barcoding approach to identify specific unknown plant samples for practical purposes (Li et al, 2009;Van de Wiel et al, 2009). Ongoing developments of new primers and improvements in sequencing techniques have facilitated the data-emergence process of plant barcoding (Soltis et al, 1996;Plunkett et al, 1997;Van de Wiel et al, 2009;Burgess et al, 2011). Recently, plant diversity belowground was determined using rbcL gene sequences as a core plant DNA barcoding marker .…”