title: GBS of Phytophthora pseudosyringae
design: Per sample, mycelium from a single Phytophthora culture was used. DNA was extracted using the Nucleospin Plant II kit (Macherey-Nagel, Dren, Germany) with extraction buffer PL1, according to the manufacturers protocol, and eluted into 50 l. GBS libraries were prepared following the approach of Elshire et al., (2011) and Poland et al., (2012), specifically using the detailed method described in Van Poucke et al. (2021). Briefly, this consisted of digestion of genomic DNA with PstI and HpaII, annealing of adaptors and barcodes, and fragment amplification. Ninety-five isolates, each with a unique barcode, were pooled and paired-end sequenced (2x150 bp) using an Illumina NovaSeq6000 (San Diego, CA, USA). The read data of the samples has been demultiplexed using GBSX v1.1.5 (Herten et al., 2015) and the adapters (including the remainder of the restriction site) trimmed using cutadapt v1.16 (Martin, 2011) and FastX toolkit v0.0.14. The forward and reverse reads were merged with PEAR v0.9.8 (Zhang et al. 2014), and then quality filtering using FastX toolkit, prinseq-lite (Schmieder and Edwards 2011), OBITOOLS v1.2.5 (Boyer et al. 2016) and pairfq 0.14.