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[…] o plasmid pKN (which carries the G418 resistance gene NEO) with the seamless assembly cloning kit (Clone Smarter Techology, USA). The gene deletion and complementation plasmids are digested and subsequent, transformed to PH-1 using the protocols described previously (Turgeon et al., ). Hygromycin B (AMRESCO USA) and geneticin (AMRESCO USA) were added to the final concentrations of 200 and 100 μg/mL, respectively, for transformant selection. Putative gene deletion and complementation mutants were identified by PCR assays with the relevant primers (Table ), and were further validated by genome sequencing performed on the HiSeq X Ten sequencing system. Reads were aligned to reference genome by Burrows-Wheeler Aligner (Li and Durbin, ). Sam alignment files were converted to bam format, sorted, and indexed with samtools (Li and Durbin, ) and then visualized by Integrative Genomics Viewer (IGV) (Thorvaldsdóttir et al., )., For conidiation assays, one mycelial plugs (9 mm in diameter) of each strain, taken from the periphery of a 3-day-old colony, were inoculated in a 50-mL flask containing 30 mL of liquid carboxymethyl cellulose (CMC). Each strain was set up in three technical repetitions. The flasks were incubated at 25°C on a shaking table (180 rpm). After 4 days of cultivation, the liquid medium was filtered through three layers of sterile lens wiping paper, and the spores were resuspended in 25 mL sterile water. The number of conidia was counted for each strain using a haemocytometer. Conidial morphology and presence of septa were observed with a Leica TCS SP5 imaging syst […]

Pipeline specifications

Software tools BWA, SAMtools, IGV
Organisms Fusarium graminearum, Triticum aestivum, Hordeum vulgare, Aspergillus fumigatus, Solanum lycopersicum