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Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata

hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorLE CAM, Bruno
dc.contributor.authorSARGENT, Dan
hal.structure.identifierLaboratoire des interactions plantes micro-organismes [LIPM]
dc.contributor.authorGOUZY, Jerome
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorAMSELEM, Joëlle
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorBELLANGER, Marie-Noëlle
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [GeT-PlaGe]
dc.contributor.authorBOUCHEZ, Olivier
dc.contributor.authorBROWN, Spencer
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorCAFFIER, Valérie
dc.contributor.authorDE GRACIA COQUEREL, Marie
hal.structure.identifierDifférenciation sexuée et méiose chez les champignons [DSMC]
hal.structure.identifierInstitut de Biologie Intégrative de la Cellule [I2BC]
hal.structure.identifierDépartement Biologie des Génomes [DBG]
dc.contributor.authorDEBUCHY, Robert
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUVAUX, Ludovic
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorPAYEN, Thibaut
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorSANNIER, Mélanie
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorSHILLER, Jason
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
hal.structure.identifierLaboratory of Phytopathology
dc.contributor.authorCOLLEMARE, Jérôme
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorLEMAIRE, Christophe
dc.date.issued2019
dc.identifier.issn2160-1836
dc.description.abstractEnThe Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.
dc.description.sponsorshipIdex Paris-Saclay
dc.language.isoen
dc.publisherGenetics Society of America
dc.subject.enapple
dc.subject.enapple scab
dc.subject.eneffectors
dc.subject.enformae specialis
dc.subject.enFusicladium
dc.subject.enMRP
dc.subject.enpear
dc.subject.entransposable elements
dc.subject.enVenturia
dc.title.enPopulation Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata
dc.typeArticle de revue
dc.identifier.doi10.1534/g3.119.400047
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalG3
bordeaux.page2405-2414
bordeaux.volume9
bordeaux.issue8
bordeaux.peerReviewedoui
hal.identifierhal-02176962
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02176962v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=G3&rft.date=2019&rft.volume=9&rft.issue=8&rft.spage=2405-2414&rft.epage=2405-2414&rft.eissn=2160-1836&rft.issn=2160-1836&rft.au=LE%20CAM,%20Bruno&SARGENT,%20Dan&GOUZY,%20Jerome&AMSELEM,%20Jo%C3%ABlle&BELLANGER,%20Marie-No%C3%ABlle&rft.genre=article


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