Detecting Diversity

High-throughput sequencing without PCR could make estimates of biodiversity more precise.

By | November 1, 2013

© GEORGE RETSECKIn the pregenomic era, biodiversity monitoring generally involved collecting species and identifying them by sight—a process fraught with human error. Once DNA sequencing became commonplace, however, this practice was largely replaced by DNA barcoding, which identifies species through their unique sequence differences at a particular gene. For instance, the most common barcoding gene used for identifying animals is mitochondrial cytochrome c oxidase subunit 1 (CO1).

Today, high-throughput next-generation sequencing enables the simultaneous barcoding of a mix of species, so that, for example, all insects collected in a trap can be processed at once. However, this approach requires PCR amplification of CO1, which introduces the potential for certain species to be over- or underrepresented when primers—small pieces of single-strand DNA that initiate PCR amplification—are better matched to one species’ DNA sequences than to another’s.

To avoid such bias, Xin Zhou and his colleagues at the research institution BGI in Shenzhen, China developed an approach that avoids PCR altogether. Instead, his team used mitochondrial enrichment to increase the proportion of CO1 DNA. Seventy-three insects from BGI’s local habitat were thrown in a blender, and the resulting soup was centrifuged at speeds that enabled isolation of a mitochondria-enriched fraction. The team then performed ultra-high-volume sequencing to recover CO1 DNA and identify the insect species present.

Even the new approach is not trouble-free, however. “It’s a good proof of concept,” says Mehrdad Hajibabaei, a professor of integrative biology at the University of Guelph in Ontario, Canada. But the increased sequencing volume necessary to compensate for the lack of PCR increases the cost, he says. (GigaScience, 2:4, 2013; published by BGI)

PCR amplification of CO1 genes followed by high-throughput sequencing 454 Genome Sequencer FLX + System ~ $100 ~ 90% No
Mitochondrial enrichment followed by high-throughput sequencing Illumina HiSeq 2000 This small-scale, proof of concept sample cost $600, but larger-scale samples may cost more. 92–97% Yes


Add a Comment

Avatar of: You



Sign In with your LabX Media Group Passport to leave a comment

Not a member? Register Now!

LabX Media Group Passport Logo

Popular Now

  1. What Budget Cuts Might Mean for US Science
    News Analysis What Budget Cuts Might Mean for US Science

    A look at the historical effects of downsized research funding suggests that the Trump administration’s proposed budget could hit early-career scientists the hardest.  

  2. UC Berkeley Receives CRISPR Patent in Europe
    Daily News UC Berkeley Receives CRISPR Patent in Europe

    The European Patent Office will grant patent rights over the use of CRISPR in all cell types to a University of California team, contrasting with a recent decision in the U.S.

  3. Opinion: On “The Impact Factor Fallacy”
  4. Unstructured Proteins Help Tardigrades Survive Desiccation
Business Birmingham