Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range
The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experiment...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1012688/full |
| _version_ | 1828142994143838208 |
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| author | Megan A. Brenes Guallar Like Fokkens Like Fokkens Martijn Rep Lidija Berke Peter van Dam |
| author_facet | Megan A. Brenes Guallar Like Fokkens Like Fokkens Martijn Rep Lidija Berke Peter van Dam |
| author_sort | Megan A. Brenes Guallar |
| collection | DOAJ |
| description | The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2. |
| first_indexed | 2024-04-11T19:49:48Z |
| format | Article |
| id | doaj.art-f44fed162a004e289c5ac3a13440c70f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T19:49:48Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f44fed162a004e289c5ac3a13440c70f2022-12-22T04:06:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.10126881012688Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host rangeMegan A. Brenes Guallar0Like Fokkens1Like Fokkens2Martijn Rep3Lidija Berke4Peter van Dam5Bioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, NetherlandsLaboratory of Phytopathology, Wageningen University, Wageningen, NetherlandsMolecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, NetherlandsMolecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, NetherlandsBioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, NetherlandsBioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, NetherlandsThe fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2.https://www.frontiersin.org/articles/10.3389/fpls.2022.1012688/fulleffectorsmimpeffector predictionhost specificitysnakemakeSIX genes |
| spellingShingle | Megan A. Brenes Guallar Like Fokkens Like Fokkens Martijn Rep Lidija Berke Peter van Dam Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range Frontiers in Plant Science effectors mimp effector prediction host specificity snakemake SIX genes |
| title | Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range |
| title_full | Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range |
| title_fullStr | Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range |
| title_full_unstemmed | Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range |
| title_short | Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range |
| title_sort | fusarium oxysporum effector clustering version 2 an updated pipeline to infer host range |
| topic | effectors mimp effector prediction host specificity snakemake SIX genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1012688/full |
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