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.

Asian wild apples threatened by gene flow from domesticated apples and by their pestified pathogen

“…In addition to the fungal collection sampled for this study, we included in our final dataset 15 V. inaequalis strains previously assigned to the pure wild type population and 18 V. inaequalis strains previously assigned to the agricultural-type population (Gladieux et al, 2010b). These 33 V. inaequalis reference strains whose genomes have been previously sequenced (Le Cam et al, 2019) had been sampled in Kazakhstan on M. sieversii , either from a peri-urban environment near Almaty (43°15000N-76°54000E) or from a natural forest site in the Tian Shan Mountains (43°13807N-77°16783E). Despite being sampled on M. sieversii , the 18 strains from the peri-urban environment clustered with strains sampled on domesticated apples in Kazakh orchards, thus belonging to the agricultural type (Gladieux et al, 2010b) (Figure 1B; Table S2).…”

“…We used the set of single nucleotide polymorphisms (SNPs) previously detected in the genomes of the 15 wild-type and 18 agricultural-type reference strains (Gladieux et al, 2010b; Le Cam et al, 2019). SNPs were filtered in order to avoid transposable elements and AT-rich regions, as well as more than 20% of missing data (Le Cam et al, 2019). After filtering, the dataset contained 1,210,121 SNPs, with no bias of missing data frequencies between wild and agricultural populations.…”

“…After filtering, the dataset contained 1,210,121 SNPs, with no bias of missing data frequencies between wild and agricultural populations. In order to identify a set of SNPs distinguishing agricultural and wild-type V. inaequalis strains, we selected 192 SNPs among the 1,210,121 available SNPs as those meeting three requirements: i) with moderate ( F ST = 0.21) to high ( F ST = 1) differentiation between wild-type and agricultural-type reference populations (Figure S1, Table S3), to obtain reasonable statistical power to assign genotypes to wild, agricultural and hybrid types, ii) physically distant enough to ensure lack of linkage disequilibrium between them (correlation coefficient between markers within population r 2 < 0.1), and iii) found in predicted genes (Le Cam et al, 2019).…”

“…To assess what allele was ancestral or derived at the SNP found to predict the host species of collection, we used five available genomes (Le Cam et al, 2019) belonging to the outgroup V. inaequalis lineage parasitising Pyracantha (Gladieux, Caffier, Devaux & Le Cam, 2010a; Le Cam, Parisi & Arene, 2002), with the following NCBI accession numbers SAMN07816619, SAMN07816620, SAMN07816621, SAMN07816617, SAMN07816618, corresponding to the strains 186, 1669, 2266, 2269 and 2507 respectively (Le Cam et al, 2019).…”

“…These parameters included migration rates in the two directions, effective sizes in the two lineages, divergence time and time elapsed since other demographic events (T AM in AM model and T SC in SC model). The ancestral effective size before the split was calculated as N ref = θ / (2 x µ x L ) (Gutenkunst et al, 2009), where θ was estimated by∂a∂i; µ is the mutation rate per nucleotide per generation, estimated to be 2 × 10 −8 from an analysis of divergence with the closely related species Venturia pirina parasitizing pear trees (Le Cam et al, 2019; data not shown). L is the effective genome length analyzed, being computed as G × s/S (Gutenkunst et al, 2009), where G is the size of the genome used, S is the total number of SNPs called in G , and s the actual number of SNPs used for inference.…”