Carl Linnaeus would be proud: A recent paper in PLoS One demonstrates the use of next-gen sequencing with genetic barcodes to accurately identify more than 100 different species from the Rodentia order. In the study, amplicons were run on the Pippin Prep from Sage Science to remove non-specific PCR products.
“Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples,” the paper from Maxime Galan, Marie Pagès, and Jean-François Cosson at the Center for Biology and Management of Populations at INRA, uses 454 GS-FLX sequencing. The authors note that correct species assignment in the diverse Rodentia order is quite challenging with morphological data alone.
In this work, the authors selected a 136 bp fragment from cytochrome b as a mini-barcode and then used it on more than 900 samples to determine its utility in accurately identifying species. Following a validation step, hundreds of samples of unknown identity were analyzed and the mini-barcode worked about 85 percent of the time, the scientists report. They also successfully tested degraded rodent DNA samples, including museum specimens and feces from rodent-eating predators.
The authors conclude, “This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.”