Whole genome sequencing with Oxford Nanopore and de novo genome assemblies of lipid-producing fungi in phylum Mucoromycota

Abstract

Phylum Mucoromycota consists of economically and ecologically important fungi, including industrial producers of lipids, enzymes and fermented foods and beverages, symbionts and decomposers of plants, as well as fungi causing post-harvest diseases and opportunistic infections in humans. The phylum includes great candidates for sustainable production lipids, but very few have so far been the subject of genomic research. In this project, the genomes of eleven lipid-producing strains were sequenced and assembled and placed phylogenetically in the phylum. Genomic DNA was extracted using bead-beating and sequenced with Oxford Nanopore Technologies’ PromethION platform. Three barcoded sequencing runs produced 62.7 gigabases and 18.9 million reads, of which 13 million reads were used to create de novo assemblies. Extracting high-quality DNA from Mucoromycota fungi is challenging. When extracting DNA for long-read sequencing, care should be taken to avoid mechanical fragmentation of the DNA and to inactivate and inhibit DNA-degrading enzymes. Despite the comparatively short read lengths resulting from degradation of the extracted DNA, the nanopore reads resulted in highly contiguous assemblies for several strains.