Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits
Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct g...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-44005-w |
| _version_ | 1797452735518343168 |
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| author | E. N. Dort E. Layne N. Feau A. Butyaev B. Henrissat F. M. Martin S. Haridas A. Salamov I. V. Grigoriev M. Blanchette R. C. Hamelin |
| author_facet | E. N. Dort E. Layne N. Feau A. Butyaev B. Henrissat F. M. Martin S. Haridas A. Salamov I. V. Grigoriev M. Blanchette R. C. Hamelin |
| author_sort | E. N. Dort |
| collection | DOAJ |
| description | Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities. |
| first_indexed | 2024-03-09T15:12:57Z |
| format | Article |
| id | doaj.art-9fbf839202454de4826c70ec8aa714b0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:12:57Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9fbf839202454de4826c70ec8aa714b02023-11-26T13:17:41ZengNature PortfolioScientific Reports2045-23222023-10-0113111510.1038/s41598-023-44005-wLarge-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traitsE. N. Dort0E. Layne1N. Feau2A. Butyaev3B. Henrissat4F. M. Martin5S. Haridas6A. Salamov7I. V. Grigoriev8M. Blanchette9R. C. Hamelin10Department of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaSchool of Computer Science, McGill UniversityPacific Forestry Centre, Canadian Forest Service, Natural Resources CanadaSchool of Computer Science, McGill UniversityDepartment of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of DenmarkInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Université de LorraineLawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome InstituteSchool of Computer Science, McGill UniversityDepartment of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaAbstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.https://doi.org/10.1038/s41598-023-44005-w |
| spellingShingle | E. N. Dort E. Layne N. Feau A. Butyaev B. Henrissat F. M. Martin S. Haridas A. Salamov I. V. Grigoriev M. Blanchette R. C. Hamelin Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits Scientific Reports |
| title | Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| title_full | Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| title_fullStr | Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| title_full_unstemmed | Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| title_short | Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| title_sort | large scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits |
| url | https://doi.org/10.1038/s41598-023-44005-w |
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