Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

Bruno Le Cam; Dan Sargent; Jérôme Gouzy; Joëlle Amselem; Marie Noëlle Bellanger; Olivier Bouchez; Spencer Brown; Valérie Caffier; Marie De Gracia; Robert Debuchy; Ludovic Duvaux; Thibaut Payen; Mélanie Sannier; Jason Shiller; Jérôme Collemare; Christophe Lemaire

doi:10.1534/g3.119.400047

Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

Bruno Le Cam, Dan Sargent, Jérôme Gouzy, Joëlle Amselem, Marie Noëlle Bellanger, Olivier Bouchez, Spencer Brown, Valérie Caffier, Marie De Gracia, Robert Debuchy, Ludovic Duvaux, Thibaut Payen, Mélanie Sannier, Jason Shiller, Jérôme Collemare, Christophe Lemaire

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

Abstract

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.

Original language	English
Pages (from-to)	2405-2414
Number of pages	10
Journal	G3: Genes, Genomes, Genetics
Volume	9
Issue number	8
DOIs	https://doi.org/10.1534/g3.119.400047
Publication status	Published - 01 Aug 2019

Keywords

Apple
Apple scab
Effectors
Elements
Formae specialis
Fusicladium
Pear
Transposable
Venturia

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10.1534/g3.119.400047

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Le Cam, B., Sargent, D., Gouzy, J., Amselem, J., Bellanger, M. N., Bouchez, O., Brown, S., Caffier, V., De Gracia, M., Debuchy, R., Duvaux, L., Payen, T., Sannier, M., Shiller, J., Collemare, J., & Lemaire, C. (2019). Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata. G3: Genes, Genomes, Genetics, 9(8), 2405-2414. https://doi.org/10.1534/g3.119.400047

Le Cam, Bruno ; Sargent, Dan ; Gouzy, Jérôme ; Amselem, Joëlle ; Bellanger, Marie Noëlle ; Bouchez, Olivier ; Brown, Spencer ; Caffier, Valérie ; De Gracia, Marie ; Debuchy, Robert ; Duvaux, Ludovic ; Payen, Thibaut ; Sannier, Mélanie ; Shiller, Jason ; Collemare, Jérôme ; Lemaire, Christophe. / Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata. In: G3: Genes, Genomes, Genetics. 2019 ; Vol. 9, No. 8. pp. 2405-2414.

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title = "Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata",

abstract = "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.",

keywords = "Apple, Apple scab, Effectors, Elements, Formae specialis, Fusicladium, Pear, Transposable, Venturia",

author = "{Le Cam}, Bruno and Dan Sargent and J{\'e}r{\^o}me Gouzy and Jo{\"e}lle Amselem and Bellanger, {Marie No{\"e}lle} and Olivier Bouchez and Spencer Brown and Val{\'e}rie Caffier and {De Gracia}, Marie and Robert Debuchy and Ludovic Duvaux and Thibaut Payen and M{\'e}lanie Sannier and Jason Shiller and J{\'e}r{\^o}me Collemare and Christophe Lemaire",

year = "2019",

month = aug,

day = "1",

doi = "10.1534/g3.119.400047",

language = "English",

volume = "9",

pages = "2405--2414",

journal = "G3: Genes, Genomes, Genetics",

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Le Cam, B, Sargent, D, Gouzy, J, Amselem, J, Bellanger, MN, Bouchez, O, Brown, S, Caffier, V, De Gracia, M, Debuchy, R, Duvaux, L, Payen, T, Sannier, M, Shiller, J, Collemare, J & Lemaire, C 2019, 'Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata', G3: Genes, Genomes, Genetics, vol. 9, no. 8, pp. 2405-2414. https://doi.org/10.1534/g3.119.400047

Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata. / Le Cam, Bruno; Sargent, Dan; Gouzy, Jérôme; Amselem, Joëlle; Bellanger, Marie Noëlle; Bouchez, Olivier; Brown, Spencer; Caffier, Valérie; De Gracia, Marie; Debuchy, Robert; Duvaux, Ludovic; Payen, Thibaut; Sannier, Mélanie; Shiller, Jason; Collemare, Jérôme; Lemaire, Christophe.

In: G3: Genes, Genomes, Genetics, Vol. 9, No. 8, 01.08.2019, p. 2405-2414.

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

TY - JOUR

T1 - Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

AU - Le Cam, Bruno

AU - Sargent, Dan

AU - Gouzy, Jérôme

AU - Amselem, Joëlle

AU - Bellanger, Marie Noëlle

AU - Bouchez, Olivier

AU - Brown, Spencer

AU - Caffier, Valérie

AU - De Gracia, Marie

AU - Debuchy, Robert

AU - Duvaux, Ludovic

AU - Payen, Thibaut

AU - Sannier, Mélanie

AU - Shiller, Jason

AU - Collemare, Jérôme

AU - Lemaire, Christophe

PY - 2019/8/1

Y1 - 2019/8/1

N2 - 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.

AB - 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.

KW - Apple

KW - Apple scab

KW - Effectors

KW - Elements

KW - Formae specialis

KW - Fusicladium

KW - Pear

KW - Transposable

KW - Venturia

UR - http://www.mendeley.com/research/population-genome-sequencing-scab-fungal-species-venturia-inaequalis-venturia-pirina-venturia-aucupa

U2 - 10.1534/g3.119.400047

DO - 10.1534/g3.119.400047

M3 - Article

VL - 9

SP - 2405

EP - 2414

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

SN - 2160-1836

IS - 8

ER -

Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

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Keywords

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