DNA extraction and sequencing procedures
DNA of the isolates from Japan and New Zealand, and the non-French European isolates was extracted using a phenol-chloroform protocol available at the JGI webpage (Isolation of genomic DNA fromPhytophthora : http://jgi.doe.gov/collaborate-with-jgi/pmo-overview/protocols-sample-preparation-information/) combined with the Qiagen Genomic tip protocol (Qiagen, Hilden, Germany). Briefly, about 500 mg fresh mycelium, from isolates grown on Serpula Capex Dox medium (see (Eastwood et al. 2011)), was flash frozen in liquid N2 and ground to powder in a mortar. Sixty mL extraction buffer (0.2 M Tris pH 8.5, 0.25 M NaCl, 25 mM EDTA, 0.5% SDS) was added to the mortar before the sample was distributed into four 50 mL tubes. 15 mL 7:3 phenol:chloroform was added to each sample, before they were mixed and incubated for 90 min at room temperature. The samples were centrifuged at 6000 G for 15 min. The aqueous phase was added to equal volume (V) of chloroform. After mixing, the samples were centrifuged for another 5 min on 6000 G. The aqueous phase was transferred to a clean tube and 0.6 V isopropanol added. The samples were incubated on ice for 30 min before centrifugation at 4 °C at 6000 G for 15 min. The pellet was washed with 20 mL 70% EtOH and dried for five min at RT. The DNA was then dissolved in 500 μL of milli-Q H2O. The four samples were pooled, 2 mg RNase A (Invitrogen) was added, and incubated for 90 min at 37 °C. Eight mL Qiagen QBT buffer was added, and the mix transferred to Genomic-tip columns and processed following the Qiagen Genomic-tip protocol. The three samples SL200, SL198 and SL265 were extracted without using the Genomic-tip protocol, according to Balasundaram et al . (2018). DNA of the French isolates was extracted using a CTAB – Qiagen genomic tip protocol as described in Payen et al . (2015).
Genomic DNA was used to construct paired-end (2 x 125 bp) libraries using SBS v4 Sample Prep Kit. Libraries were sequenced using the Illumina HiSeq 2500 platform (Illumina, Inc., San Diego, CA, USA) at the GeT-PlaGe sequencing facility (Toulouse, France). For the isolates SL200, SL198 and SL265 (2 x 108 bp) libraries were sequenced on the Illumina GAII at the SNP&SEQ Technology Platform (Uppsala, Sweden).