Nav: Home

Building a DNA barcode library for the Canadian flora using herbarium collections

February 13, 2018

The dry, mothball-scented stacks of a herbarium might seem to be far away from the cutting edge of plant science. However, the curated plant specimens stored there contain irreplaceable genetic, morphological, ecological, and chemical information just waiting to be analyzed with modern techniques. In a new study in a recent issue of Applications in Plant Sciences, Dr. Maria Kuzmina at the University of Guelph and colleagues tapped this trove of information, showing that herbarium specimens can yield viable DNA barcode libraries.

A DNA barcode library is a kind of molecular identification key that compiles DNA sequence (the "barcode") from each species in the library, focusing on a few well-studied, easily sequenced genomic regions. This allows future researchers to sample the DNA from an unknown species, sequence these regions, and easily find which species the sample came from by comparing the sequence to the library.

"These references are used for forensic identification of samples with a single DNA source, including direct identification of the plants if morphological characters are unavailable," said Dr. Kuzmina. They are also "in great demand in metagenomic projects for both practical and theoretical questions, like analyzing plant supplements and food, or environmental DNA in soil and water."

Other studies, including those by Dr. Kuzmina, have previously demonstrated that herbarium specimens can produce DNA barcode libraries. This study stands apart in its scale, providing barcodes for 98% of the vascular plant species in Canada (5,076 of the 5,190). In total, the authors examined 13,170 individual specimens from 27 herbaria across Canada and the northern United States, supplemented by 7,660 freshly collected specimens. The scale of sampling makes the resulting DNA barcode library more powerful for species identification, because query sequences are less likely to match an incorrect, closely related reference species if the correct species is also present in the library.

To assist future researchers in making use of herbarium resources, the authors also quantified the factors that influence DNA degradation in herbarium specimens. Unsurprisingly, the authors found that factors such as age and method of preservation affected the level of DNA degradation. They also found that the family to which the species belongs matters, because compounds present in some families but not others could affect DNA degradation.

"Our analysis is based on a large sample, which was parsed not only by age, but also by taxonomic affiliation, and we found that some groups of plants are capable of preserving DNA for a really long time," said Dr. Kuzmina. "The oldest specimen we succeeded to recover the DNA barcodes for our collection was collected in 1849. It belonged to lady's mantle (Alchemilla) from the rose family."

As Dr. Kuzmina and colleagues demonstrated, the genetic information stored in herbaria is an important resource for the 21st century. "In the herbarium you find specimens carefully collected, identified, and catalogued by several generations of professional field botanists, across the entire country, during all vegetative seasons, including distant areas, and rare findings," said Dr. Kuzmina.

The high-quality curation and identification of each reference specimen by experts, and the traceability of each reference sequence back to a physical specimen lends the barcode library a level of taxonomic authority that only a herbarium can. "Annotated by experts, this material provides unparalleled source of references for those who perform molecular studies," said Dr. Kuzmina. "Without the fundamental knowledge about biodiversity the cutting edge sciences cannot operate."
-end-


Botanical Society of America

Related Dna Articles:

Penn State DNA ladders: Inexpensive molecular rulers for DNA research
New license-free tools will allow researchers to estimate the size of DNA fragments for a fraction of the cost of currently available methods.
It is easier for a DNA knot...
How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of biological systems?
How do metals interact with DNA?
Since a couple of decades, metal-containing drugs have been successfully used to fight against certain types of cancer.
Electrons use DNA like a wire for signaling DNA replication
A Caltech-led study has shown that the electrical wire-like behavior of DNA is involved in the molecule's replication.
Switched-on DNA
DNA, the stuff of life, may very well also pack quite the jolt for engineers trying to advance the development of tiny, low-cost electronic devices.
Researchers are first to see DNA 'blink'
Northwestern University biomedical engineers have developed imaging technology that is the first to see DNA 'blink,' or fluoresce.
Finding our way around DNA
A Salk team developed a tool that maps functional areas of the genome to better understand disease.
A 'strand' of DNA as never before
In a carefully designed polymer, researchers at the Institute of Physical Chemistry of the Polish Academy of Sciences have imprinted a sequence of a single strand of DNA.
Doubling down on DNA
The African clawed frog X. laevis genome contains two full sets of chromosomes from two extinct ancestors.
'Poring over' DNA
Church's team at Harvard's Wyss Institute for Biologically Inspired Engineering and the Harvard Medical School developed a new electronic DNA sequencing platform based on biologically engineered nanopores that could help overcome present limitations.

Related Dna Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Bias And Perception
How does bias distort our thinking, our listening, our beliefs... and even our search results? How can we fight it? This hour, TED speakers explore ideas about the unconscious biases that shape us. Guests include writer and broadcaster Yassmin Abdel-Magied, climatologist J. Marshall Shepherd, journalist Andreas Ekström, and experimental psychologist Tony Salvador.
Now Playing: Science for the People

#513 Dinosaur Tails
This week: dinosaurs! We're discussing dinosaur tails, bipedalism, paleontology public outreach, dinosaur MOOCs, and other neat dinosaur related things with Dr. Scott Persons from the University of Alberta, who is also the author of the book "Dinosaurs of the Alberta Badlands".