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Genome assembly of the fungus Leucoagaricus gongylophorus cultivated by the ant Atta colombica using long-read MinION sequences

Pepijn Wilhelmus Kooij, Pepijn Wilhelmus Kooij
Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, United Kingdom; Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, United Kingdom
Assembling heterogenous (two very different sets of chromosomes) or polyploid (more than two sets of chromosomes) genomes can be challenging, but in a fast-developing world, new techniques and software are regularly developed. Leaf-cutting ants cultivate a polyploid fungus with an average of 7 different genomes which has proven to be difficult to assemble using regular short-read genome sequencing. In this study, I used the Oxford Nanopore Technologies MinION to produce long-read sequences of Leucoagaricus gongylophorus cultivated by the ant Atta colombica . I then used a series of different software packages to assemble genomes from long-read sequences (CANU and Nanopolish) as well as software to deal with heterogeneous and polyploid species (Redundans). The quality of the assemblies was tested by extracting a core set of single-copy genes using BUSCO. With this, I developed a pipeline to assemble fungal genomes accurately using long-read sequences. The resulting genome assembly is an improvement of the one currently available and gives new insights into this intriguing mutualism between ants and fungi. Furthermore, I was able to fully assemble the fungal mitochondrial genome with a high coverage (±4000X), which can be used to both understand the mechanistic of this fungus, but which can also be used for more accurate phylogenetic analyses. In conclusion, I was able to show cost-efficient methods and a pipeline to accurately assemble fungal genomes, that can be used for a wide variety of analyses.