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).
1. Zhou X; et al., Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification GigaScience 2013 2:4
2. Zhou, X; Li, Y; Liu, S; Yang, Q; Su, X; Zhou, L; Tang, M; Fu, R; Li, J (2013): NGS biodiversity data. GigaScience Database http://dx.doi.org/10.5524/100045 (Provides raw data, assembly and annotation results.)
3. Zhou, X; Li, Y; Liu, S; Yang, Q; Su, X; Zhou, L; Tang, M; Fu, R; Li, J; Huang, Q (2013): NGS Biodiversity software. GigaScience Database http://dx.doi.org/10.5524/100046 (Provides software and supporting material.)
4. Barcode of Life http://www.barcodeoflife.org
Editor, GigaScience, BGI Hong Kong
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Bicheng Yang, Ph.D.
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GigaScience (http://www.gigasciencejournal.com) is co-published by BGI, the world's largest genomics institute, and BioMed Central, the world's largest open-access publisher. The journal covers research that uses or produces 'big data' from the full spectrum of the life sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, it is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB (http://gigadb.org), as well as in their publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and will be integrating a data analysis platform and cloud resources into the database later this year, maximizing the potential utility and re-use of data. (Follow us on twitter @GigaScience; sina-weibo http://weibo.com/gigasciencejournal, and keep up-to-date on our blogs http://blogs.openaccesscentral.com/blogs/gigablog/feed/entries/rss).
BGI, a China-based scientific institution, was founded in 1999 and has since become the largest genomic organization in the world. With a focus on research and applications in the healthcare, agriculture, conservation, and bio-energy fields, BGI has a proven track record of innovative, high profile research, which has generated over 178 publications in top-tier journals such as Nature and Science. It also contributes to scientific communication by publishing the international research journal GigaScience and hosting its associated database GigaDB. BGI's distinguished achievements have made a great contribution to the development of genomics in both China and the world. Their goal is to make leading-edge genomics highly accessible to the global research community by integrating industry's best technology, economies of scale, and expert bioinformatics resources. BGI and its affiliates, BGI-Americas and BGI-Europe, have established partnerships and collaborations with leading academic and government research institutions, as well as global biotechnology and pharmaceutical companies. (Follow BGI on twitter @BGI_events.)
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