Wednesday, January 27, 2016

The Ultimate Identifier



Editor's Note: This is the first in a series of videos we will release in 2016 about the use of scientific collections and DNA technology.

When it comes to reliable plant identification in their work, Ida Lopez and Dr. Caroline Puente, of the Smithsonian’s National Museum of Natural History (NMNH) Plant DNA Barcoding Project, botany department, have a tool most associate with the retail world. But barcodes, in this case DNA barcodes, are creating many research opportunities in the scientific world in areas of ecology, evolution, conservation and more.

A DNA barcode, which is made up of approximately 600 base pairs of the species’ entire genome, can authentically identify down to the species level. A commonly used barcode marker in animals is the mitochondrial gene cytochrome oxidase 1 (CO1). This gene however does not successfully identify plant species.

“We knew that in animals the CO1 site was very indicative,” Lopez said. “Zoologists could just sequence this one site and tell exactly what type of animal it was.”

Because the CO1 gene has evolved slower in plants, it is not useful to identify plant species. So around 10 years ago, researchers, under the direction of John Kress, NMNH Department of Botany curator, began looking for candidate genes in plants. They found that they needed a combination of at least two chloroplast regions - rbcL and trnH-psbA - to create a workable plant DNA barcode. Today matK, another chloroplast gene, and a nuclear region – the Internal Transcribed Spacer (ITS) are added to insure success.

While researchers agree that fresh tissue is ideal for extracting DNA, Puente said that in cases where scientists can’t revisit a location to collect samples, museum collections, in this case botanical specimens, are invaluable.

“One of the big advantages of DNA barcoding is that we do not need a lot of tissue material” Puente said. “... You can barcode small organisms such as insects and bacteria - anything that has DNA even in limited amounts.”

A tissue sample just a little larger than a pencil eraser is enough for DNA extraction and barcoding. Lopez and Puente have specimens at their fingertips in the Department of Botany’s vast collection at NMNH. The collection holds 5 million specimens, with approximately 105,000 of those serving as type specimens.

To learn more about Lopez and Puente's work, visit The Plant DNA Barcode Project.


References
W. John Kress, Carlos GarcĂ­a-Robledo, Maria Uriarte, and David L. Erickson (2014, November 19). DNA barcodes for ecology, evolution, and conservation. CellPress, vol 30 (1): 25-35. doi: 10.1016/j.tree.2014.10.008

What is DNA Barcoding? Barcode of Life. Retrieved from http://www.barcodeoflife.org/content/about/what-dna-barcoding 

W. John Kress, David L. Erickson. (2007, June 6) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLOSOne(6): e508. doi: 10.1371/journal.pone.0000508

Search the Department of Botany Collections. Smithsonian National Museum of Natural History. Retrieved from http://collections.nmnh.si.edu/search/botany/

Plant DNA Barcode Project. Smithsonian National Museum of Natural History. Retrieved from http://botany.si.edu/projects/DNAbarcode/


Glossary

type specimens
The representative for an animal or plant species, which acts as a reference point when a species is first named.

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