- A new genomics technique for studying biodiversity with bulk-collected insects opens new horizons for how we study biodiversity and our local environment -
Hong Kong, China – BGI and BioMed Central’s open access journal GigaScience 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 more accurate and quantitative version of a new biodiversity analysis technique called metabarcoding. Further, the analyses in the article revealed how diverse and poorly characterized insect communities (or diversity) can be, even from two small sites within the researchers’ own backyard— literally.
Combining DNA barcoding, which utilizes a standard gene fragment for species identification with next generation sequencing (NGS) technologies; previous metabarcoding methods, however, have required a step to amplify the amount of DNA collected 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 assessing species diversity, it also allows the researcher to determine the total quantity of mitochondrial DNA present for each species, making it possible to reveal relative abundance and biomass of each species, which is important information in 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).
BGI was founded in Beijing, China, in 1999 with the mission to become a premier scientific partner for the global research community. The goal of BGI is to make leading-edge genomic science highly accessible, which it achieves through its investment in infrastructure, leveraging the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.
BGI has a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research: research that has generated over 200 publications in top-tier journals such as Nature and Science. BGI’s many accomplishments include: sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and the 2011 German deadly E. coli outbreak, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, more recently, the human Gut Metagenome, as well as a significant proportion of the genomes for the1000 Genomes Project.
For more information, please visit www.genomics.cn and www.bgiamericas.com.
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
Before 27th March proof version available here: http://tinyurl.com/squishome
After 27th March, published version will be available here: http://dx.doi.org/10.1186/2047-217X-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
l: +852 3610 3531
Mob: +852 92490853
Bicheng Yang, Ph.D.
Public Communication Officer
Joyce Peng, Ph.D.