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Squished bug genomics: Insect goo aids biodiversity research
Date:3/26/2013

March 27th, 2013, Hong Kong, China GigaScience (a BGI and BioMed Central open access journal) announces the publication of an article that presents a new method for assessing and understanding biodiversity that uses a DNA-soup made from crushed-up insects and next generation sequencing technology. This bulk-collected insect goo has the potential to rapidly and cost-effectively reveal the diversity and make-up of both known and unknown species collected in a particular time and place. The new method devised by Xin Zhou and colleagues at BGI Shenzhen, China, is a more accurate and quantitative version of a new biodiversity analysis technique called metabarcoding. Further, the analyses in the article revealed how poorly characterized and diverse insect communities can be, even from two small sites within the researchers' own backyard literally.

The work here combines DNA barcoding, which utilizes a standard gene fragment for species identification, with next generation sequencing (NGS) technologies; previous metabarcoding methods, however, have required a DNA-amplification step that uses the polymerase chain reaction (PCR). This step can introduce problematic errors into the analysis. Xin Zhou and colleagues have found a way to carry out this method without this step, giving the method the potential to be far more accurate. In addition to being able to assess species diversity, it also allows the researcher to determine the total quantity of mitochondrial DNA present for each species. This makes it possible to reveal the relative abundance and biomass of each species, which is important information for ecological studies.

Allowing more consistent and rapid sampling, this new technique may simplify the study of changes in biodiversity over space and time. Dr. Neil Davies, Director of the University of California Berkeley's Gump South Pacific Research, who studies model ecosystems stated: "PCR-free metabarcoding could transform the way we study ecosystems and monitor biodiversity".

What Truly Lies in Your Own Backyard:

In testing the technique on species collected on a hillside behind their laboratory, the authors were very surprised by what they managed to find in their own neighborhood. BGI, the world's largest genomics organization, is situated on the edge of Shenzhen, a city of 12 million people in the Pearl River delta one of the most densely urbanized regions in the world. Setting up two traps close to each not only revealed how much diversity there was, but also detected species not currently present in online databases. The findings demonstrated how little is known about insect diversity in China, and by opening up the ability to carry out these types of systematic and high-throughput analyses we should now be able to test if this is the case every where else in the world.

Of the study, Dr. Zhou said: "The 2 sampling sites were very close to each other, yet there were only around 10% of the total species being shared between them. The fact that only very few of our barcoded specimens received a sequence match from the Barcode of Life Data Systems, the world's largest barcode reference database, suggests that much of China's arthropod fauna still remains as a mystery, at least from a molecular aspect."

With the ability to detect and discover tiny organisms, stomach contents and partial samples without the usual visual cues, Dr. Zhou adds, "In some sense, the contribution of NGS technology to biodiversity research is equivalent to what microscopes did to microbiology."

To boost the transparency and usability of this new method, and in keeping with the scientific community's goals of making all data fully and freely available, all data and tools/pipelines from this project are publically available as citable entries in the GigaScience database, GigaDB. Raw data is also available as raw reads in the SRA (Accession # SRA067357).


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Contact: Scott Edmunds
scott@gigasciencejournal.com
852-361-03531
GigaScience
Source:Eurekalert

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