Population Genome Sequencing of the Scab Fungal Species <i>Venturia inaequalis</i> , <i>Venturia pirina</i> , <i>Venturia aucupariae</i> and <i>Venturia asperata</i>

Abstract

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