Dataset Information

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

ABSTRACT: Premise of the study:Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. Methods:Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery. Results:Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae). Discussion:Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.

SUBMITTER: Kuzmina ML

PROVIDER: S-EPMC5749818 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Kuzmina Maria L ML Braukmann Thomas W A TWA Fazekas Aron J AJ Graham Sean W SW Dewaard Stephanie L SL Rodrigues Anuar A Bennett Bruce A BA Dickinson Timothy A TA Saarela Jeffery M JM Catling Paul M PM Newmaster Steven G SG Percy Diana M DM Fenneman Erin E Lauron-Moreau Aurélien A Ford Bruce B Gillespie Lynn L Subramanyam Ragupathy R Whitton Jeannette J Jennings Linda L Metsger Deborah D Warne Connor P CP Brown Allison A Sears Elizabeth E Dewaard Jeremy R JR Zakharov Evgeny V EV Hebert Paul D N PDN

Applications in plant sciences 20171222 12

<h4>Premise of the study</h4>Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.<h4>Methods</h4>Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions ...[more]

PMID: 29299394

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Project description:BackgroundBecause 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.ResultsThis 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.ConclusionsOur results provided fast and cost-effective solution to create a comprehensive, effective DNA barcode reference library for a local flora.

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Dataset Information

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Publications

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

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