Genome‐wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families
Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animal...
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Published in | Molecular plant pathology Vol. 22; no. 1; pp. 31 - 47 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
England
John Wiley & Sons, Inc
01.01.2021
Wiley John Wiley and Sons Inc |
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Abstract | Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.
Alternative splicing occurs in the plant‐pathogenic fungus Sclerotinia sclerotiorum during colonization of diverse host plants and could generate functional diversity in the repertoire of secreted proteins. |
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AbstractList | Abstract
Sclerotinia sclerotiorum
is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of
S. sclerotiorum
with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of
S. sclerotiorum
and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487
S. sclerotiorum
genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified
S. sclerotiorum
genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus
S. sclerotiorum
during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by
S. sclerotiorum
during infection. Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection. Mol Plant Pathol. 2020;00:1-17. | 1 wileyonlinelibrary.com/journal/mpp 1 | INTRODUC TI ON Sclerotinia sclerotiorum is a plant-parasitic fungus that causes white mould disease. It is known for its aggressive necrotrophic lifestyle, which means that the fungus actively kills the plant host cells and thrives by feeding on the dead plant material, and for exhibiting a broad host range. S. sclerotiorum can infect more than 600 host plants including economically important species such as tomato Abstract Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection. K E Y W O R D S alternative splicing, computational analysis, host adaptation, isoforms, RNA sequencing (RNA-seq), Sclerotinia sclerotiorum Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection. Alternative splicing occurs in the plant‐pathogenic fungus Sclerotinia sclerotiorum during colonization of diverse host plants and could generate functional diversity in the repertoire of secreted proteins. Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection. Alternative splicing occurs in the plant‐pathogenic fungus Sclerotinia sclerotiorum during colonization of diverse host plants and could generate functional diversity in the repertoire of secreted proteins. Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3' receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection. |
Audience | Academic |
Author | Kusch, Stefan Ibrahim, Heba M.M. Raffaele, Sylvain Didelon, Marie |
AuthorAffiliation | 3 Present address: Plant Health and Protection Division of Plant Biotechnics Department of Biosystems Faculty of Bioscience Engineering KU Leuven Leuven Belgium 1 LIPM, Université de Toulouse INRAE CNRS Castanet‐Tolosan France 2 Genetics Department Faculty of Agriculture Cairo University Giza Egypt 4 Present address: Unit of Plant Molecular Cell Biology Institute for Biology I RWTH Aachen University Aachen Germany |
AuthorAffiliation_xml | – name: 1 LIPM, Université de Toulouse INRAE CNRS Castanet‐Tolosan France – name: 2 Genetics Department Faculty of Agriculture Cairo University Giza Egypt – name: 4 Present address: Unit of Plant Molecular Cell Biology Institute for Biology I RWTH Aachen University Aachen Germany – name: 3 Present address: Plant Health and Protection Division of Plant Biotechnics Department of Biosystems Faculty of Bioscience Engineering KU Leuven Leuven Belgium |
Author_xml | – sequence: 1 givenname: Heba M.M. orcidid: 0000-0003-0603-7755 surname: Ibrahim fullname: Ibrahim, Heba M.M. email: heba.ibrahim@kuleuven.be organization: Cairo University – sequence: 2 givenname: Stefan orcidid: 0000-0002-2472-5255 surname: Kusch fullname: Kusch, Stefan organization: CNRS – sequence: 3 givenname: Marie orcidid: 0000-0002-8458-8117 surname: Didelon fullname: Didelon, Marie organization: CNRS – sequence: 4 givenname: Sylvain orcidid: 0000-0002-2442-9632 surname: Raffaele fullname: Raffaele, Sylvain email: sylvain.raffaele@inrae.fr organization: CNRS |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33111422$$D View this record in MEDLINE/PubMed https://hal.inrae.fr/hal-03007953$$DView record in HAL |
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Copyright | 2020 The Authors. published by British Society for Plant Pathology and John Wiley & Sons Ltd 2020 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd. COPYRIGHT 2021 John Wiley & Sons, Inc. 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Attribution - NonCommercial - NoDerivatives |
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Keywords | RNA sequencing (RNA-seq) Sclerotinia sclerotiorum isoforms host adaptation computational analysis alternative splicing |
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Snippet | Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The... Abstract Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The... Mol Plant Pathol. 2020;00:1-17. | 1 wileyonlinelibrary.com/journal/mpp 1 | INTRODUC TI ON Sclerotinia sclerotiorum is a plant-parasitic fungus that causes... Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The... |
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StartPage | 31 |
SubjectTerms | Alternative splicing Colonization computational analysis Fungi Gene expression Genes Genetic research Genomes Genomics host adaptation Host plants Infections Introns isoforms Kinases Life Sciences Original Parameter identification Pathogens Proteins Ribonucleic acid RNA RNA sequencing (RNA‐seq) Sclerotinia sclerotiorum Signal transduction Splicing Virulence |
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Title | Genome‐wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families |
URI | https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fmpp.13006 https://www.ncbi.nlm.nih.gov/pubmed/33111422 https://www.proquest.com/docview/2471193386 https://hal.inrae.fr/hal-03007953 https://pubmed.ncbi.nlm.nih.gov/PMC7749757 |
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