Population genome sequencing of the scab fungal speciesVenturia inaequalis,Venturia pirina,Venturia aucupariaeandVenturia asperata

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.3

Chromosome-level genome reference ofVenturia effusa, causative agent of pecan scab

“…The AT-rich regions are extremely gene-poor, containing only 0.15% of the protein coding genes despite comprising 24.7% of the genome. This is similar to the genome structure seen in other Venturia species, most notably the genomes of V. inaequalis, which on average have 45.3% AT-rich sequence (Le Cam et al 2019). This type of genome structure was first described in fungi for Leptosphaeria maculans (Rouxel et al 2011).…”

“…At present, there are more than 90 genome assemblies available for Venturia species, representing an active research area of fungal genomics. However, many of the genomes are highly fragmented ranging from 66 scaffolds to more than 40,000 (Bock et al 2016b;Chen et al 2017;Deng et al 2017;Passey et al 2018;Johnson et al 2019;Le Cam et al 2019;Prokchorchik et al 2019). Here, we present the first entire and finished genome sequence for the genus Venturia.…”

“…Although other Venturia genomes have been sequenced (Bock et al 2016b;Chen et al 2017;Deng et al 2017;Passey et al 2018;Johnson et al 2019;Le Cam et al 2019;Prokchorchik et al 2019), the complete genome sequence of V. effusa FRT5LL7-Albino represents the first chromosomal level assembly of a Venturia species. This valuable resource is a basis for scientists in the Venturia research community to advance the comparative genomics of scab pathogens; it is a useful resource for the identification of effectors, will provide insights into the epidemiology and population biology of the pathogens, and the evolution of the genus Venturia.…”

Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

“…However, there are other fungal pathogens with even greater repeat content (>62%) such as Venturia and Blumeria species (Cam et al, 2019;Castanera et al, 2016;Frantzeskakis et al, 2018;Peter et al, 2016;Wöstemeyer & Kreibich, 2002). Many of Bsal's repeats are transposable elements (TEs) (19.36%) which underpin the genome expansion described in other species including the fungal wheat pathogen Zymoseptoria tritici, the barley powdery mildew, Blumeria graminis f.sp.…”

New North American Isolates of Venturia inaequalis Can Overcome Apple Scab Resistance of Malus floribunda 821

“…The program Trimmomatic(Bolger et al 2014) was used to remove the sequencing adaptors and low-quality reads with quality score below 20. The genome assembly of V. inaequalis strain EU-B04 VeinUTG001 (LeCam et al 2019) was retrieved from National Center for Biotechnology Information (NCBI) genome database and used to align the high-quality reads from the previous step. The alignments were filtered to eliminate PCR duplicated sequences and a sorted binary alignment format (BAM) was obtained for each sample using SAMtools(Li et al 2009).…”