Environmental metagenomics with next generation sequencing. 2009-11 SAGES and Soybean Rust Sampling Network. Lacombe. Agassiz. Saskatoon. Ottawa. Beloeil. Morden. St. Clotilde. Morrisburg. Forest. Harrington, PEI. Toronto. 350 air and rain samples processed
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2009-11 SAGES and Soybean Rust Sampling Network
350 air and rain samples processed
60M DNA barcode sequences (bacteria & fungi)
JB: rain is filtered directly in the field through a filter (0.45uM or 8uM)
BK: air samples collected directly into a sterile tube
YE: rainwater is collected in a bucket, vacuum-filtered in the labthrough a 0.45 µm filter
Matching barcode sequences from environment to references
Gaps in collections and taxonomy
DNA barcodes (>50K/ sample)
NGS DNA sequencers
* Collector running for one week.
DNA sequenced every 4 week.
5 samples processed per summer.
2007-9 also available, but less sites.
Sampler efficiency in trueFungi - total number of sequences on left and ratio between 3 sites
GENOMICS R&D INITIATIVEQuarantine and Invasive Species ProjectPATRICE BOUCHARD AND ANDRÉ LÉVESQUEAgriculture and Agri-Food CanadaNovember 21, 2012CFIA Plant Business Line Committee meeting
Building targeted reference libraries of genetic data (Barcodes) to aquatic and terrestrial organisms of greatest concern to Canada
Libraries will ultimately be made available to the national and international scientific community
Develop focused metagenomic approaches for the direct detection of invasive species from complex environmental samples
PCR amplify with universal markers (e.g. 16S, ITS, cpn60, COI, matK)
GRDI Barcode of Life Database (BOLD)
BOLD at Guelph, iBOL and GenBank
RNA/DNA whole genomes
Distribution of species of associated with agriculture primarily found in each country
Number of species shared with Eurasia is lower than among our three countries and impact of introduction is higher between continents
Each dot represents a known or putative new species
Sample numbers: Imported from Asia = 8; Canadian samples = 130
Grain samples imported from Asia
Total of 32,307 OTU’s
Canadian grain samples
OTU’s absent in Canada: Potential alien risk for NA crops if becomes established
OTU’s present in Canada but absent in imports tested so far: Potential risk for NA trade
Present both in Canada and in imports – low risk
Native species Trichalophusgranicollis
Regulated pest Otiorhynchusligustici
Photos from Patrice Bouchard, AAFC Ottawa, Coordinator of GRDI project