Molecular pathology selected abstracts

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Editors: Donna E. Hansel, MD, PhD, chair of pathology, Oregon Health and Science University, Portland; Richard D. Press, MD, PhD, professor and director of molecular pathology, OHSU; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Sounak Gupta, MBBS, PhD, senior associate consultant, Mayo Clinic, Rochester, Minn.; Tauangtham Anekpuritanang, MD, molecular pathology fellow, Department of Pathology, OHSU; Hassan Ghani, MD, molecular genetic pathology fellow, Department of Pathology, OHSU; and Fei Yang, MD, assistant professor, Department of Pathology, OHSU. 

Role of DNA barcodes in discovering species and their role in ecosystems

August 2019—As sequencing technology becomes faster and less expensive and devices become smaller and more portable, the application of DNA sequencing to various branches of science is rapidly expanding. Advances in this technology have, for example, led to the development of portable genomic laboratories that use fast, inexpensive, and portable DNA sequencers for species identification. The Earth is estimated to have between 8.7 million and 20 million types of plants, animals, and fungi, but only about 1.8 million of them have been given formal descriptions. The task of species identification historically has relied heavily on morphologic phenotyping performed by a limited pool of skilled taxonomists. More recently, however, DNA sequencing was introduced as a tool to further characterize species. Various DNA targets, such as ribosomal DNA (rDNA), single nucleotide polymorphisms (SNPs), and evolutionarily conserved genes have been sequenced and ascribed to known species as taxon “barcodes,” the name applied to the stretches of DNA sequenced. In 2003, Paul Hebert, et al., at the University of Guelph, in Canada, proposed using the mitochondrial gene cytochrome c oxidase I (COI ) as the basis for a global bioidentification system for animals. By that time, robust universal primers were available for the gene, allowing representatives of most animal phyla to be tested. The later finding that COI possessed a greater range of phylogenetic signal than any other mitochondrial gene cemented COI as the target of choice for many bioidentification efforts. In 2015, the International Barcode of Life (IBOL) consortium, an alliance of research organizations spearheaded by Hebert, completed its Barcode 500K project by assembling DNA barcode records for 500,000 species in five years. The data from Barcode 500K populate part of the International Barcode of Life Database, which has widespread application in areas ranging from the food industry, where it’s used for identifying food allergens and tracking foods and food labeling, to forensic entomology, in which anthropod colonization is used to estimate the postmortem interval. IBOL’s Bioscan program, a seven-year effort that was slated to begin this summer, will gather specimens and study species interactions worldwide with the intent of expanding IBOL’s reference library by 15 million barcode records. Other teams from around the globe are also adopting this approach to comb samples for new species in their labs or in the field. Rudolf Meier, PhD, and colleagues at the National University of Singapore are using the recently developed MinION nanopore sequencing system to catalog biodiversity in Singapore. Costing less than $1,000 and approximately the size of a smartphone, the sequencing system can be paired with a battery-powered mini polymerase chain reaction thermocycler and a laptop loaded with informatics software to allow mobile sequencing in the field. Duke University scientist Lydia Greene, PhD, and colleagues recently published a field study conducted in the Madagascar dry forest, in which they used the barcoding system on a lemur sample and decided on the spot whether it was likely to be from a new species. With the growth of species barcode databases, IBOL proposes a next-level analysis in which sequence characterization of a single specimen can disclose its commensals, mutualists, and parasites. Taken further, metabarcoding to examine the species composition of 100,000 bulk samples from sites worldwide has been proposed as a first step in compiling comprehensive regional biodiversity baselines. As sequencing costs decrease and bioinformatics optimization progresses, DNA barcoding will serve as the underpinning for global biodiversity monitoring and discovery.

Chimeno C, Moriniere J, Podhorna J, et al. DNA barcoding in forensic entomology—establishing a DNA reference library of potentially forensic relevant arthropod species. J Forensic Sci. 2019;64(2):593–601.

Correspondence: Caroline Chimeno at ca_chimeno@yahoo.com

Collins RA, Cruickshank RH. The seven deadly sins of DNA barcoding. Mol Ecol Resour. 2013;13(6):969–975.

Correspondence: Dr. R. A. Collins at rupertcollins@gmail.com

Hebert PDN, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes. Proc Biol Sci. 2003;270(1512):313–321.