Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | LE CAM, Bruno | |
| dc.contributor.author | SARGENT, Dan | |
| hal.structure.identifier | Laboratoire des interactions plantes micro-organismes [LIPM] | |
| dc.contributor.author | GOUZY, Jerome | |
| hal.structure.identifier | Unité de Recherche Génomique Info [URGI] | |
| dc.contributor.author | AMSELEM, Joëlle | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | BELLANGER, Marie-Noëlle | |
| hal.structure.identifier | Génome et Transcriptome - Plateforme Génomique [GeT-PlaGe] | |
| dc.contributor.author | BOUCHEZ, Olivier | |
| dc.contributor.author | BROWN, Spencer | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | CAFFIER, Valérie | |
| dc.contributor.author | DE GRACIA COQUEREL, Marie | |
| hal.structure.identifier | Différenciation sexuée et méiose chez les champignons [DSMC] | |
| hal.structure.identifier | Institut de Biologie Intégrative de la Cellule [I2BC] | |
| hal.structure.identifier | Département Biologie des Génomes [DBG] | |
| dc.contributor.author | DEBUCHY, Robert | |
| hal.structure.identifier | Biodiversité, Gènes & Communautés [BioGeCo] | |
| dc.contributor.author | DUVAUX, Ludovic | |
| hal.structure.identifier | Interactions Arbres-Microorganismes [IAM] | |
| dc.contributor.author | PAYEN, Thibaut | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | SANNIER, Mélanie | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | SHILLER, Jason | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| hal.structure.identifier | Laboratory of Phytopathology | |
| dc.contributor.author | COLLEMARE, Jérôme | |
| hal.structure.identifier | Institut de Recherche en Horticulture et Semences [IRHS] | |
| dc.contributor.author | LEMAIRE, Christophe | |
| dc.date.issued | 2019 | |
| dc.identifier.issn | 2160-1836 | |
| dc.description.abstractEn | The 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.sponsorship | Idex Paris-Saclay | |
| dc.language.iso | en | |
| dc.publisher | Genetics Society of America | |
| dc.subject.en | apple | |
| dc.subject.en | apple scab | |
| dc.subject.en | effectors | |
| dc.subject.en | formae specialis | |
| dc.subject.en | Fusicladium | |
| dc.subject.en | MRP | |
| dc.subject.en | pear | |
| dc.subject.en | transposable elements | |
| dc.subject.en | Venturia | |
| dc.title.en | Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata | |
| dc.type | Article de revue | |
| dc.identifier.doi | 10.1534/g3.119.400047 | |
| dc.subject.hal | Sciences du Vivant [q-bio] | |
| bordeaux.journal | G3 | |
| bordeaux.page | 2405-2414 | |
| bordeaux.volume | 9 | |
| bordeaux.issue | 8 | |
| bordeaux.peerReviewed | oui | |
| hal.identifier | hal-02176962 | |
| hal.version | 1 | |
| hal.popular | non | |
| hal.audience | Internationale | |
| hal.origin.link | https://hal.archives-ouvertes.fr//hal-02176962v1 | |
| bordeaux.COinS | ctx_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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