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De novo Genome Assembly and Annotation of 12 Fungi Associated with Fruit Tree Decline Syndrome in ON, Canada

Summary

Apple and stone fruit trees in Ontario have been dying at alarming rates since 2016. Researchers sequenced and analyzed the genetic code of 12 different fungi suspected of causing this decline. This study provides the first complete genetic blueprints for several fungal species, helping farmers and scientists better understand what causes the disease and develop ways to prevent it.

Background

Apple and stone fruit trees in Ontario have experienced alarming mortality rates since 2016, with up to 42% mortality in apples and 72% in stone fruits. The exact cause of Fruit Tree Decline (FTD) and Rapid Apple Decline (RAD) remains elusive, though pathogenic fungi, viruses, and abiotic stressors are implicated.

Objective

To sequence, assemble, and annotate the genomes of 12 fungi associated with FTD and RAD syndromes in Ontario, Canada. The study aims to provide genomic resources for understanding molecular mechanisms of decline and developing disease management strategies.

Results

The study presents the first assembled and annotated genomes for three ascomycete species: Diplodia intermedia, Diatrype stigma, and Nothophoma quercina, plus high-quality reference genomes for Diplodia seriata, Didymella pomorum, and Neofusicoccum ribis. All 12 genomes achieved >97% BUSCO completeness with comprehensive functional annotations identifying protein-coding genes, biosynthetic gene clusters, and secreted proteins.

Conclusion

These genomic resources significantly enhance understanding of fungal pathogenicity in fruit tree decline and support development of targeted disease management strategies. The availability of these assemblies enables downstream analyses including effector identification and comparative genomics for resistance breeding and integrated disease management.
  • Published in:Scientific Data,
  • Study Type:Genomics Study,
  • Source: 10.1038/s41597-025-05192-5; PMID: 40593868
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