Genome Sequencing and Assembly of Fungal Isolate

For sequencing, DNA of IPO94269 and 16 ascospores was isolated using a phenol-chloroform extraction protocol as described previously (Sambrook and Russell, 2001 ). Library preparation and sequencing using a Pacific Biosciences Sequel for IPO94269 and Illumina HiSeq3000 machine for 16 ascospore-derived colonies were performed at the Max Planck-Genome-centre, Cologne, Germany. Reads have been deposited in the Sequence Read Archive and are available under the BioProject PRJNA438050. Assembly of the IPO94269 genome was conducted at the Max Planck-Genome-center, Cologne using the software suite HGAP 4 (Chin et al., 2016 (link)) from Pacific Biosciences with the default settings. Synteny analysis was conducted with SyMAP version 4.2 (Soderlund et al., 2006 (link); Soderlund et al., 2011 (link)) (Figure 1—figure supplement 1). Illumina reads of the ascospores were filtered and mapped to the reference genome of IPO323 (Goodwin et al., 2011 (link)) as previously described (Habig et al., 2017 (link)) in which the transposable elements were masked (Grandaubert et al., 2015 (link)).