Population Genome Sequencing of the Scab Fungal Species , , and .

The genus comprises fungal species that are pathogens on host plants, including and on apple, on sorbus and on pear. Although the genetic structure of populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 strains that represent each species and each population within We present a PacBio genome assembly for the EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of and 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 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 pathogens. Especially, it will help understanding the evolutionary history of species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.