Full chromosome assembly of symbiotic fungal genomes from complex metagenomics samples using nanopore sequencing

Growing fungi in axenic culture is challenging, slow, or impossible for many species. Furthermore, fungi frequently occur embedded in diverse microorganismal communities. Shotgun sequencing samples from nature yields rich and complex metagenomes, and assembling target fungal genome from such samples can be challenging.

Here Jessica L. Allen used nanopore sequencing to assemble genomes of five species of lichenized fungi from five different families. Whole lichen extracts were sequenced and genomes assembled from complex, metagenomic data. All genomes were high quality, and one genome (Lepraria neglecta) was assembled to whole chromosomes. Nanopore sequencing is a promising approach for generating high-quality references genomes in non-model and hard to culture fungi.