Using Herbarium‐Derived DNAs to Assemble a Large‐Scale DNA Barcode Library for the Vascular Plants of Canada

Kuzmina, Maria L.; Braukmann, Thomas; Fazekas, Aron J.; Graham, Sean W.; deWaard, Stephanie; Rodrigues, Anuar; Bennett, Bruce; Dickinson, Timothy A.; Saarela, Jeffery M.; Catling, Paul M.; Newmaster, Steven G.; Percy, Diana M.; Fenneman, Erin; Lauron-Moreau, Aurélien; Ford, Bruce A.; Gillespie, Lynn J.; Ragupathy, Subramanyam; Whitton, Jeannette; Jennings, Linda; Metsger, Deborah A.; Warne, Connor P; Brown, Angela Demke; Sears, Elizabeth; deWaard, Jeremy R; Zakharov, Evgeny; Hebert, Paul D. N.

doi:10.3732/apps.1700079

Cited by 55 publications

(61 citation statements)

References 78 publications

(87 reference statements)

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“…We used standard protocols to bidirectionally sequence five markers commonly used for plant DNA barcoding: rbcL, matK, trnL-F, trnH-psbA, and ITS (protocols in Text S1; primers in Table S1) (Fazekas, Kuzmina, Newmaster, & Hollingsworth, 2012;Ivanova, Fazekas, & Hebert, 2008;Kartzinel et al, 2015;Kuzmina et al, 2017). Sequences (N = 4,696) from a subset of specimens that we collected between 2012 and 2015 were initially included in a reference library used to support a DNA-metabarcoding study of herbivore diets (Kartzinel et al, 2015).…”

Section: Generation Of Dna Barcodesmentioning

confidence: 99%

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Gill

Musili

Kurukura

et al. 2019

Molecular Ecology Resources

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Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA‐barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL‐F, trnH–psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra‐ and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack “barcode gaps”, defined as disparities between the maximum intra‐ and minimum interspecific genetic distances. We found barcode gaps for 72%–89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode‐gap presence or absence for all of the markers in combination and for matK, trnL‐F, and trnH–psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.

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Section: Generation Of Dna Barcodesmentioning

confidence: 99%

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Gill

Musili

Kurukura

et al. 2019

Molecular Ecology Resources

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“…Ranunculaceae and Caryophyllaceae were the families with the poorest barcoding performance among old samples. Previously, Kuzmina et al (2017) have also observed difference in specimen age effects among plant families.…”

Section: Resultsmentioning

confidence: 74%

“…Only in Papaveraceae, the success rate was 100% for both barcoding regions. Previously, Kuzmina et al (2017) have observed great differences in barcoding success among plant families, especially concerning the matK barcode, where the used primers are not fully universal. Among very old samples, 17 were collected between years 1867 and 1899.…”

Section: Resultsmentioning

confidence: 99%

“…It was also recorded whether a species was native (including archaeophytes) or introduced (definitions following Hämet-Ahti et al 1998). All plant samples were shipped to the Canadian Centre for DNA Barcoding for DNA extraction, PCR and sequencing of chloroplast matK and rbcL barcodes using standard plant barcoding protocols (Ivanova et al 2008;Kuzmina and Ivanova 2011;Kuzmina et al 2017). All barcodes, images and other sample informations are available in BOLD (http://www.bolds ystem s.org) under the FinBOL-Plants (FBPL) project (https ://doi.org/10.5883/ ds-fbpl1 ).…”

Section: Sampling and Barcodingmentioning

confidence: 99%

“…It has been well documented that DNA is often well preserved in herbarium samples and, therefore, can be used for DNA analyses, such as sequencing in molecular systematic and phylogenetic studies, and DNA barcoding (e.g., Lehtonen and Christenhusz 2010;von Cräutlein et al 2011;Xu et a. 2015;Kuzmina et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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The effects of sample age and taxonomic origin on the success rate of DNA barcoding when using herbarium material

Korpelainen

Pietiläinen

2019

Plant Syst Evol

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We have produced DNA barcodes for Finnish plant taxa. In this study, we specifically report the barcoding success for herbarium materials varying widely in age, also paying attention on success rate variation and genetic distances among different plant families. Additionally, we investigated whether the level of intraspecific variation differs between native and introduced species. The specimens had been collected between years 1867 and 2013. Among all studied specimens, the average success rates for any barcode (matK or rbcL), rbcL, matK and both barcodes equaled 81, 79, 55 and 53%, respectively, and among species (at least one specimen per species barcoded successfully) 95, 95, 74 and 73%, respectively. We found significant age effects on the barcoding success, the greatest decline being visible in over 100-year-old samples. Plant families showed differences in overall success rates and sample age effects, as well as in intraspecific and interspecific variation levels, while the average level of intraspecific variation appeared similar among native and introduced species. Besides being valuable for the identification of species, DNA barcoding with sufficient sampling is also a tool to investigate specific evolutionary questions, such as biogeographic patterns or the adaptive capacity of invasive and other alien plant species.

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Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds

2018

Self Cite

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Premise of the StudyThe detection of environmental DNA (eDNA) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring.MethodsA protocol was developed to detect pondweeds in water samples using atpB‐rbcL and ITS2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario (RARE). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank.ResultsWe detected two species earlier documented at the experimental site during ecological surveys (Potamogeton crispus and Stuckenia pectinata) and three species new to the RARE checklist (P. foliosus, S. filiformis, and Zannichellia palustris).DiscussionOur targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats.

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Using Herbarium‐Derived DNAs to Assemble a Large‐Scale DNA Barcode Library for the Vascular Plants of Canada

Cited by 55 publications

References 78 publications

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

The effects of sample age and taxonomic origin on the success rate of DNA barcoding when using herbarium material

Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds

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