Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresens...

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Autores: Gramaje, David, Berlanas, Carmen, Martínez-Diz, M. P., Díaz-Losada, Emilia, Antonielli, Livio, Beier, Sabrina, Gorfer, Markus, Schmoll, Monika, Compant, Stéphane
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/233090
Acceso en línea:http://hdl.handle.net/10261/233090
Access Level:acceso abierto
Palabra clave:Black-foot disease
High-throughput next generation sequencing
Vitis vinifera L.
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spelling Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyleGramaje, DavidBerlanas, CarmenMartínez-Diz, M. P.Díaz-Losada, EmiliaAntonielli, LivioBeier, SabrinaGorfer, MarkusSchmoll, MonikaCompant, StéphaneBlack-foot diseaseHigh-throughput next generation sequencingVitis vinifera L.The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusariumfujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.The research was funded by CAR (Government of La Rioja, Spain), under the project “Development of Microsatellite Markers to Study the Genetic Diversity of Dactylonectria torresensis Populations in Spain” (project number R-05-18).Molecular Diversity Preservation InternationalGobierno de La RiojaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2021202120202021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/233090reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.3390/jof6040255Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2330902026-05-22T06:33:51Z
dc.title.none.fl_str_mv Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
title Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
spellingShingle Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
Gramaje, David
Black-foot disease
High-throughput next generation sequencing
Vitis vinifera L.
title_short Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
title_full Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
title_fullStr Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
title_full_unstemmed Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
title_sort Comparative genomic of Dactylonectria torresensis strains from grapevine, soil and weed highlights potential mechanisms in pathogenicity and endophytic lifestyle
dc.creator.none.fl_str_mv Gramaje, David
Berlanas, Carmen
Martínez-Diz, M. P.
Díaz-Losada, Emilia
Antonielli, Livio
Beier, Sabrina
Gorfer, Markus
Schmoll, Monika
Compant, Stéphane
author Gramaje, David
author_facet Gramaje, David
Berlanas, Carmen
Martínez-Diz, M. P.
Díaz-Losada, Emilia
Antonielli, Livio
Beier, Sabrina
Gorfer, Markus
Schmoll, Monika
Compant, Stéphane
author_role author
author2 Berlanas, Carmen
Martínez-Diz, M. P.
Díaz-Losada, Emilia
Antonielli, Livio
Beier, Sabrina
Gorfer, Markus
Schmoll, Monika
Compant, Stéphane
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Gobierno de La Rioja
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Black-foot disease
High-throughput next generation sequencing
Vitis vinifera L.
topic Black-foot disease
High-throughput next generation sequencing
Vitis vinifera L.
description The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusariumfujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.
publishDate 2020
dc.date.none.fl_str_mv 2020
2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/233090
url http://hdl.handle.net/10261/233090
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.3390/jof6040255
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Molecular Diversity Preservation International
publisher.none.fl_str_mv Molecular Diversity Preservation International
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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