Email updates

Keep up to date with the latest news and content from BMC Ecology and BioMed Central.

Open Access Methodology article

Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library

Maria L Kuzmina1*, Karen L Johnson2, Hannah R Barron3 and Paul DN Hebert1

Author affiliations

1 Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada

2 The Manitoba Museum, Botany Department, Manitoba, Canada

3 Trent University, Environmental and Life Sciences, Peterborough, ON, Canada

For all author emails, please log on.

Citation and License

BMC Ecology 2012, 12:25  doi:10.1186/1472-6785-12-25

Published: 28 November 2012

Abstract

Background

Because arctic plant communities are highly vulnerable to climate change, shifts in their composition require rapid, accurate identifications, often for specimens that lack diagnostic floral characters. The present study examines the role that DNA barcoding can play in aiding floristic evaluations in the arctic by testing the effectiveness of the core plant barcode regions (rbcL, matK) and a supplemental ribosomal DNA (ITS2) marker for a well-studied flora near Churchill, Manitoba.

Results

This investigation examined 900 specimens representing 312 of the 354 species of vascular plants known from Churchill. Sequencing success was high for rbcL: 95% for fresh specimens and 85% for herbarium samples (mean age 20 years). ITS2 worked equally well for the fresh and herbarium material (89% and 88%). However, sequencing success was lower for matK, despite two rounds of PCR amplification, which reflected less effective primer binding and sensitivity to the DNA degradation (76% of fresh, 45% of herbaria samples). A species was considered as taxonomically resolved if its members showed at least one diagnostic difference from any other taxon in the study and formed a monophyletic clade. The highest species resolution (69%) was obtained by combining information from all three genes. The joint sequence information for rbcL and matK distinguished 54% of 286 species, while rbcL and ITS2 distinguished 63% of 285 species. Discrimination of species within Salix, which constituted 8% of the flora, was particularly problematic. Despite incomplete resolution, the barcode results revealed 22 misidentified herbarium specimens, and enabled the identification of field specimens which were otherwise too immature to identify. Although seven cases of ITS2 paralogy were noted in the families Cyperaceae, Juncaceae and Juncaginaceae, this intergenic spacer played an important role in resolving congeneric plant species at Churchill.

Conclusions

Our results provided fast and cost-effective solution to create a comprehensive, effective DNA barcode reference library for a local flora.

Keywords:
Arctic; DNA barcoding; rbcL; matK; ITS2; Species resolution; Climate change; Biomonitoring