Genomic sequencing indicates non‐random mating ofVenturia inaequalisin a mixed cultivar orchard

Abstract

Apple scab is one of the most economically important diseases of apples worldwide. The disease is caused by the haploid ascomycete Venturia inaequalis. Growing apples in cultivar mixtures may reduce disease severity. To determine how the pathogen population structure is affected by host mixtures we studied 24 V. inaequalis isolates sampled from three different apple cultivars (Bramley, Cox, and Worcester) growing in a mixed orchard approximately 50 years old. The isolates were aligned against a reference genome and single nucleotide polymorphisms (SNPs) were called between the isolates. The populations isolated from Bramley and Worcester were distinct, while Cox isolates were an admixture. This supports previous tests of the ability of isolates to cross‐infect hosts, and molecular comparisons using simple sequence repeats (SSRs). Genotype‐specific allele (GSA) loci were not distributed randomly across contigs in proportion to contig length, but were clustered. Clustered GSA loci were observed in almost all contigs. This indicates population differentiation across the whole genome, presumably due to lack of crossing‐over events between Bramley and Worcester isolates. This lack is probably due to physical separation effects: sexual mating is more likely to take place and succeed between isolates from lesions on the same leaf than from contact between independently infected leaves in leaf litter on the orchard floor. This would especially be the case if sexual reproduction is initiated before leaf‐fall.

TheVenturia inaequaliseffector repertoire is expressed in waves and is dominated by expanded families with predicted structural similarity to avirulence proteins from other plant-pathogenic fungi

“…So far, however, there have been no publications describing the cloning of Avr effector genes from V. inaequalis. Crucially, the genomes of multiple V. inaequalis isolates have been sequenced [18][19][20][21][22][23] and bioinformatic studies have identified a large catalogue of secreted, non-enzymatic proteinaceous effector candidates (ECs) from which candidate Avr effectors can be identified [19]. Most of these ECs belong to expanded (sequence-related) families [19]; however, the driving force behind the expansion of these families is not yet known.…”

Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

“…Population differentiation was also observed in isolates collected from the same orchard from different apple host cultivars (Passey et al, 2020). Rvi6 (formerly known as Vf), from Malus floribunda clone 821, is the most frequently used apple scab resistance gene in apple breeding (Papp et al, 2020).…”

“…Genome sequence reads of V. inaequalis isolates from BioProjects PRJNA407103 (Le Cam et al, 2019) and PRJNA354841 (Passey et al, 2020) were downloaded from NCBI using the SRA toolkit (https://trace.ncbi.nlm.nih.gov/Trace s/sra/sra.cgi?view=toolk it_doc). BioProjects PRJNA407103 (Le Cam et al, 2019) and PRJNA354841 (Passey et al, 2020) contain sequence reads of V. inaequalis (n = 103), V. asperata (n = 3), V. aucuparia (n = 1) and V. pirina (n = 3) representing 16 countries across North and South America, Europe and Asia.…”

“…Genome sequence reads of V. inaequalis isolates from BioProjects PRJNA407103 (Le Cam et al, 2019) and PRJNA354841 (Passey et al, 2020) were downloaded from NCBI using the SRA toolkit (https://trace.ncbi.nlm.nih.gov/Trace s/sra/sra.cgi?view=toolk it_doc). BioProjects PRJNA407103 (Le Cam et al, 2019) and PRJNA354841 (Passey et al, 2020) contain sequence reads of V. inaequalis (n = 103), V. asperata (n = 3), V. aucuparia (n = 1) and V. pirina (n = 3) representing 16 countries across North and South America, Europe and Asia. BioProject PRJNA407103 used singlestrain isolation (Le Cam et al, 2019), BioProject PRJNA354841 used single-lesion sampling with clone correction (Passey et al, 2020) and the newly sequenced North American samples used singlespore isolation for DNA extraction and sequencing.…”

CRISPR-Cas9 gene editing and rapid detection of gene-edited mutants using high-resolution melting in the apple scab fungus,Venturia inaequalis

“…A key development over recent years has been the availability of several V. inaequalis genome sequences and gene catalogues (2, 5–9), as well as the development of both polyethylene glycol (PEG)-mediated protoplast and Agrobacterium tumefaciens -mediated transformation protocols for use with this fungus (10). However, while several V. inaequalis genes of interest that are putatively involved in the infection process of apple have been identified (5, 11–15), none have been functionally characterized to date using traditional gene deletion or disruption techniques.…”