The
Venturia
genus comprises fungal species that are pathogens on
Rosaceae
host plants, including
V. inaequalis
and
V. asperata
on apple,
V. aucupariae
on sorbus and
V. pirina
on pear. Although the genetic structure of
V. inaequalis
populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87
Venturia
strains that represent each species and each population within
V. inaequalis
. We present a PacBio genome assembly for the
V. inaequalis
EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of
V. inaequalis
and
V. aucupariae
contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of
V. inaequalis
presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of
Venturia
pathogens. Especially, it will help understanding the evolutionary history of
Venturia
species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.