In-house long read sequencing yields affordable superb fungal genome assemblies

Filamentous fungi are known to produce a wide range of secondary metabolites that are of food, agrochemical and pharmaceutical interest. The traditional way to discover novel secondary metabolites from fungi is to screen the compounds produced under permissive conditions. However, this is quite tedious and labor intensive since numerous conditions must be screened for each fungus and still no guarantee of achieving permissive conditions exist. An alternative approach is whole genome sequencing followed by genome mining based on predictions of conserved domains, which can be utilized to identify secondary metabolite gene clusters of interest – thus predicting the synthesis potential of filamentous fungi. Promising candidate gene clusters can then be transferred and overexpressed in heterologous production hosts or laborious screening of growth conditions can be undertaken on a limited and qualified set of fungi.

In this poster, we present an in-house and affordable sequencing pipeline utilizing the MinION platform from Oxford Nanopore Technologies for the cost-efficient sequencing of hundreds filamentous fungi. Recent advancements in MinION sequencing technology and bioinformatics data analyses enables quick and straightforward long-read sequencing and highly contiguous assemblies with a low error rate. In relation to genome mining in fungi, an added benefit of long-read sequencing is that single reads spanning entire gene clusters can usually be found, providing experimental validation of the candidate gene clusters. Thus eliminating the possibility of artefact chimeric gene cluster made by assembly of short reads.