2.2 | P. fijiensis isolates, DNA extraction and sequencing
Mycelium cultures initiated by single ascospore isolated from necrotic lesions were identified as belonging to P. fijiensis and stored as described in Zapater et al. 2008. Genomic DNA was extracted from mycelium cultures as detailed in Halkett et al. 2010. Equimolar amounts of DNA from isolates of each population were then pooled (see details in Table 1) to reduce variation during pool sequencing (Pool-Seq), as suggested by Rode et al. 2018. The mean pool size of the six and eight populations collected in 2011 and 2013 was, respectively, 42.25 and 93.12 individuals per pool. The pools of isolates collected in 2011 were sequenced as described in Carlier et al. 2021b, at the Genome Quebec Innovation Centre at McGill University on a GAII platform for paired-end Illumina sequencing (read length of 100 pb, target depth of 80X). The pools of isolates collected in 2013 were sequenced for this study by Genewiz UK Ltd for paired-end HiSeq for paired-end Illumina sequencing (read length of 150 pb, target depth of 200X). Finally, the DNAs of 63 isolates sampled in the location Villa Clara in 2011 were sequenced for this study at the Genome Quebec Innovation Centre at McGill University for individual paired-end Illumina sequencing (read length of 100 pb, target depth of 30X).