A genome resource for several North American Venturia inaequalis isolates with multiple fungicide resistance phenotypes

Authors: LICHTNER, FRANZ - Orise Fellow; Jurick, Wayne; AYER, KATRIN - Cornell University; Gaskins, Verneta; VILLANI, SARA - North Carolina State University; COX, KERIK - Cornell University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2019
Publication Date: 11/13/2019
Citation: Lichtner, F.J., Jurick II, W.M., Ayer, K.M., Gaskins, V.L., Villani, S.M., Cox, K.D. 2019. Venturia inaequalis genomes with multiple fungicide resistance phenotypes causing preharvest apple scab and postharvest pinpoint scab. Phytopathology. https://doi.org/10.1094/PHYTO-06-19-0222-A.
DOI: https://doi.org/10.1094/PHYTO-06-19-0222-A

Interpretive Summary: With a farm gate value estimated at nearly 4 billion, the US apple industry relies on blemish free fruit for direct consumption and export. However, the apple scab fungus causes losses and impacts fruit quality in the field and during storage. Fungicides are the main control strategy and prevalence of fungicide resistant populations results in losses for growers. Hence, a detailed understanding of the genetic basis of fungicide resistance in the apple scab fungus, Venturia inaequalis, is important to aid resistance management strategies and prolong effective disease control. Our study utilized whole genome sequencing of 4 scab isolates and we deciphered all the genes and their putative functions using computer programs. We found that the various genomes showed differences in their size and other hallmarks that can help explain their resistance to different, commonly used fungicides in the field. Our data will help other researchers explore genetic differences in genes responsible for fungicide resistance in the apple scab fungus. Additionally, our findings can facilitate further research to develop rapid detection strategies that will guide fungicide applications for effective control while minimizing unnecessary applications of materials, thus reducing grower cost and minimizing environmental impact.

Technical Abstract: The apple scab pathogen, Venturia inaequalis, is amongst the most economically important fungal pathogens that effects apples both pre and postharvest. Fungicide applications are an essential part of disease management, coupled with implementation of cultural practices, and genetic sources of resistance in the host. Here we present for the first time the sequencing, detailed annotation, and analysis of four North American V. inaequalis whole genomes having both sensitive and multiple fungicide resistance phenotypes. The assembled genomes ranged in size from 39.9 Mb to 61.5 Mb, which are within the range of published Venturia spp. genomes, though smaller than the reference genome of 72.3 Mb. The predicted gene models through GeneMark-ES and AUGUSTUS were annotated using multiple approaches including InterproScan 5.1, SignalP 4.1, Phobius, CAZy and antiSMASH. The number of scaffolds ranged from 619-7555 greater than 500bp and containing 12225-12628 unique genes based on QUAST. The genome completeness determined with the BUSCO v3 Ascomycota odb9 database including 1315 targets resulting in 1259-1282 benchmarking universal single copy orthologs. Initial gene annotations through a Diamond blastP search of the UniProt database version 2018_09 resulted in 581-601 valid annotations. An analysis of the predicted secretome with SignalP resulted in 1381-1401 annotations and the number of transposable elements detected ranged from 48 to 153. The differences observed herein provide opportunities for further investigation into the mechanisms involved in fungicide resistance as transposons may be driving genome diversity, overall genome size, and or enabling fungicide resistance in the field under various selection pressures.