Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

Bruno Le Cam, Dan Sargent, Jérôme Gouzy, Joëlle Amselem, Marie Noëlle Bellanger, Olivier Bouchez, Spencer Brown, Valérie Caffier, Marie De Gracia, Robert Debuchy, Ludovic Duvaux, Thibaut Payen, Mélanie Sannier, Jason Shiller, Jérôme Collemare, Christophe Lemaire

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)2405-2414
Number of pages10
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number8
DOIs
Publication statusPublished - 01 Aug 2019

Keywords

  • Apple
  • Apple scab
  • Effectors
  • Elements
  • Formae specialis
  • Fusicladium
  • Pear
  • Transposable
  • Venturia

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