Geographic atlas of mycotoxigenic fungi through metagenomic surveys of DNA barcodes using a novel taxonomic classification approach

Citation

Chen, W., C. Visagie, M. Liu, K. Seifert, T. Graefenhan, S. Hambleton and C. A. Levesque (2016). Geographic atlas of mycotoxigenic fungi through metagenomic surveys of DNA barcodes using a novel taxonomic classification approach. 2016 Canadian Phytopathological Society (CPS) annual meeting, June 12-15, 2016, Moncton, New Brunswick.

Plain language summary

Mycotoxins are toxic secondary metabolites produced by species of fungal genera such as Alternaria, Aspergillus, Claviceps, Fusarium and Penicillium. This study aims to identify mycotoxigenic fungi from environmental samples collected from Canada, China and France. We use a in-house bioinformatics tool, named AODP to design signature oligonucleotides and then probed target species from large amplicon-NGS databases. This approach improved classification accuracy in comparison with off-the-shelf bioinformatics tools used by majority of the community. We will develop a living atlas of mycotoxigenic fungi in the three countries and to discover cryptic/novel species in the five genera, which may have the potential becoming emerging pathogen if long-distance dispersal occurs.

Abstract

Mycotoxins are toxic secondary metabolites produced by species of fungal genera such as Alternaria, Aspergillus, Claviceps, Fusarium and Penicillium. Species of one genus often produce different biosynthetic groups of mycotoxins, which have adverse health effects on human and livestock. Some of these species are considered pathogens of agricultural/medical importance. For risk assessment and mycotoxin management, it is important to accurately identify these organisms. This is challenging for Metagenomic surveys using DNA barcodes. The internal transcribed spacer (ITS) of the rDNA region is the official fungal barcode, but often lacks sufficient discriminatory power at the species/subspecies ranks. Furthermore, existing algorithms for sequence classification are similarity- and composition-based, which are imprecise for taxonomic profiling below the genus level and for accommodating the inherent error rate of various Next Generation Sequencing (NGS) platforms. Our three objectives were: 1) using clades-specific oligonucleotides to facilitate and improve species/subspecies-level interpretation of metabarcodes; 2) developing a living geographic atlas of mycotoxin producing fungi in Canada; 3) discovering known and putatively unknown species and provide critical information to taxonomists for species discovery and reference database development. A total of 45 million ITS1 and ITS2 454-pyro-tagged sequences from air/rain samples and commodity seed wash samples collected during 2009–2013 were compared with the curated UNITE fungal ITS database. Preliminary results showed that ITS1 and ITS2 recovered different numbers of putative species (Operational Taxonomic Unit, OTU) at 97% similarity cutoff, with ITS2 recovering almost double the OTUs for Aspergillus, Penicillium and Claviceps.

Publication date

2016-06-12

Author profiles