Fungal Genomic Library Construction and Sequencing

Fungal strains were grown in potato dextrose broth for 1 wk and conidia were harvested for DNA isolation according to Epstein et al (25 (link)). Genomic libraries were constructed using the QIA Seq FX DNA library kit according to instructions from Qiagen Inc. Sequencing was performed on either the Illumina HiSeq 4000 or the PacBio Sequel II HiFi platform at the University of California Davis, Genome Center. Illumina sequence data were assessed using FastQC for per base and sequence quality score, GC content, and sequence length distribution. Low-quality reads were removed and adapters were trimmed using Trimmomatic v36 (65 (link)), and error correction was performed using ALLPATHS-LG (66 (link)). Draft genome assemblies were obtained using A5 (67 (link)). Genome completeness was assessed using the Sordariomyceta odb9 set of BUSCO (v3) (38 ). Contigs representing potential contaminant data were identified using FCS-GX, developed by the National Center for Biotechnology Information and available with documentation at https://github.com/ncbi/fcs/wiki/FCS-GX. Putative contaminant contigs were removed, except in cases where pangenome orthology searches identified bonafide (>95% identity) F. oxysporum genes. PacBio data were assembled using Hifiasm v0.16.0 using the program’s default parameters (68 (link)).