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).