Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Joelle J. Amselem
(1, 2)
,
Christina A. Cuomo
(3)
,
Jan A. L. van Kan
(4)
,
Muriel Viaud
(2)
,
Ernesto P. Benito
(5)
,
Arnaud Couloux
(6)
,
Pedro M Coutinho
(7)
,
Ronald P. de Vries
(8, 9)
,
Paul S. Dyer
(10)
,
Sabine, Helma Fillinger-David
(2)
,
Elisabeth Fournier
(2, 11)
,
Lilian Gout
(2)
,
Matthias Hahn
(12)
,
Linda Kohn
(13)
,
Nicolas Lapalu
(1)
,
Kim M. Plummer
(14)
,
Jean-Marc Pradier
(2)
,
Emmanuel Quevillon
(1, 15)
,
Amir Sharon
(16)
,
Adeline Simon
(2)
,
Arjen ten Have
(17)
,
Bettina Tudzynski
(18)
,
Paul Tudzynski
(18)
,
Patrick Wincker
(6)
,
Marion Andrew
(13)
,
Véronique Anthouard
(6)
,
Ross E. Beever
(19)
,
Rolland Beffa
(15)
,
Isabelle Benoit
(8)
,
Ourdia Bouzid
(8)
,
Baptiste Brault
(2, 1)
,
Zehua Chen
(3)
,
Mathias Choquer
(2, 20)
,
Jerome Collemare
(21, 22)
,
Pascale Cotton
(22)
,
Etienne Danchin
(23)
,
Corinne da Silva
(6)
,
Angelique Gautier
(2)
,
Corinne Giraud-Delville
(2)
,
Tatiana Giraud
(24)
,
Celedonio Gonzalez
(25)
,
Sandrine Grossetete
(15)
,
Ulrich Gueldener
(26)
,
Bernard Henrissat
(7)
,
Barbara J. Howlett
(27)
,
Chinnappa Kodira
(3)
,
Matthias Kretschmer
(12)
,
Anne Lappartient
(15)
,
Michaela Leroch
(12)
,
Caroline Levis
(2)
,
Evan Mauceli
(3)
,
Cécile Neuvéglise
(28)
,
Birgitt Oeser
(18)
,
Matthew Pearson
(3)
,
Julie Poulain
(6)
,
Nathalie Poussereau
(20)
,
Hadi Quesneville
(1)
,
Christine Rascle
(29)
,
Julia Schumacher
(18)
,
Béatrice Segurens
(6)
,
Adrienne Sexton
(27)
,
Evelyn Silva
(30)
,
Catherine Sirven
(15)
,
Darren M. Soanes
(31)
,
Nicholas J. Talbot
(31)
,
Matt Templeton
(32)
,
Chandri Yandava
(3)
,
Oded Yarden
(33)
,
Qiandong Zeng
(3)
,
Jeffrey A. Rollins
(34)
,
Marc-Henri Lebrun
(2, 1, 15)
,
Marty Dickman
(35)
1
URGI -
Unité de Recherche Génomique Info
2 BIOGER - BIOlogie et GEstion des Risques en agriculture
3 BROAD INSTITUTE - Broad Institute of MIT and Harvard
4 WUR - Wageningen University and Research [Wageningen]
5 Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias
6 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
7 AFMB - Architecture et fonction des macromolécules biologiques
8 Kluyver Centre for Genomics of Industrial Fermentations
9 CBS-KNAW - Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre
10 School of Biology
11 UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite
12 Faculty of Biology
13 Biology Department
14 Botany Department
15 MAP - Microbiologie, adaptation et pathogénie
16 Department of Molecular Microbiology and Biotechnology
17 IIB - Instituto de Investigaciones Biológicas [Mar del Plata]
18 Molekularbiologie und Biotechnologie der Pilze
19 Manaaki Whenua – Landcare Research [Lincoln]
20 FungiPath - Génomique fonctionnelle des champignons pathogènes des plantes
21 Laboratory of Phytopathology
22 Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes
23 IBSV - Interactions Biotiques et Santé Végétale
24 ESE - Ecologie Systématique et Evolution
25 Departamento de Bioquímica y Biología Molecular
26 HMGU - Helmholtz Zentrum München = German Research Center for Environmental Health
27 School of Botany [Melbourne]
28 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
29 CNRS - Centre National de la Recherche Scientifique
30 Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas
31 School of Biosciences
32 Plant and Food Research
33 Department of Plant Pathology and Microbiology
34 Department of Plant Pathology
35 Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology
2 BIOGER - BIOlogie et GEstion des Risques en agriculture
3 BROAD INSTITUTE - Broad Institute of MIT and Harvard
4 WUR - Wageningen University and Research [Wageningen]
5 Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias
6 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
7 AFMB - Architecture et fonction des macromolécules biologiques
8 Kluyver Centre for Genomics of Industrial Fermentations
9 CBS-KNAW - Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre
10 School of Biology
11 UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite
12 Faculty of Biology
13 Biology Department
14 Botany Department
15 MAP - Microbiologie, adaptation et pathogénie
16 Department of Molecular Microbiology and Biotechnology
17 IIB - Instituto de Investigaciones Biológicas [Mar del Plata]
18 Molekularbiologie und Biotechnologie der Pilze
19 Manaaki Whenua – Landcare Research [Lincoln]
20 FungiPath - Génomique fonctionnelle des champignons pathogènes des plantes
21 Laboratory of Phytopathology
22 Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes
23 IBSV - Interactions Biotiques et Santé Végétale
24 ESE - Ecologie Systématique et Evolution
25 Departamento de Bioquímica y Biología Molecular
26 HMGU - Helmholtz Zentrum München = German Research Center for Environmental Health
27 School of Botany [Melbourne]
28 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
29 CNRS - Centre National de la Recherche Scientifique
30 Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas
31 School of Biosciences
32 Plant and Food Research
33 Department of Plant Pathology and Microbiology
34 Department of Plant Pathology
35 Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology
Joelle J. Amselem
- Function : Correspondent author
Christina A. Cuomo
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- Function : Correspondent author
- PersonId : 969418
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Jan A. L. van Kan
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- Function : Correspondent author
- PersonId : 969419
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Muriel Viaud
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- Function : Correspondent author
- PersonId : 743813
- IdHAL : muriel-viaud
- ORCID : 0000-0001-8341-0555
- IdRef : 188613897
Connectez-vous pour contacter l'auteur
Sabine, Helma Fillinger-David
- Function : Author
- PersonId : 180195
- IdHAL : sabine-fillinger
- ORCID : 0000-0003-4683-0803
- IdRef : 126838445
Elisabeth Fournier
- Function : Author
- PersonId : 736524
- IdHAL : elisabeth-fournier
- ORCID : 0000-0001-6959-1855
- IdRef : 16443741X
Lilian Gout
- Function : Author
- PersonId : 13202
- IdHAL : lilian-gout
- ORCID : 0000-0002-8432-1834
- IdRef : 126749396
Nicolas Lapalu
- Function : Author
- PersonId : 1207128
- IdHAL : nlapalu
- ORCID : 0000-0002-9773-4611
Adeline Simon
- Function : Author
- PersonId : 1244407
- IdHAL : adeline-simon
- ORCID : 0000-0002-0020-6442
Patrick Wincker
- Function : Author
- PersonId : 757160
- IdHAL : patrick-wincker
- ORCID : 0000-0001-7562-3454
Baptiste Brault
- Function : Author
- PersonId : 956927
Mathias Choquer
- Function : Author
- PersonId : 749946
- IdHAL : mathias-choquer
- ORCID : 0000-0002-3768-160X
Etienne Danchin
- Function : Author
- PersonId : 734755
- IdHAL : danchin-etienne-gj
- ORCID : 0000-0003-4146-5608
- IdRef : 083014454
Corinne da Silva
- Function : Author
- PersonId : 908690
- IdHAL : corinne-da-silva
Corinne Giraud-Delville
- Function : Author
- PersonId : 745649
- IdHAL : corinne-giraud-delville
Tatiana Giraud
- Function : Author
- PersonId : 738377
- IdHAL : tatiana-giraud
- ORCID : 0000-0002-2685-6478
- IdRef : 097392278
Bernard Henrissat
- Function : Author
- PersonId : 833340
Cécile Neuvéglise
- Function : Author
- PersonId : 183393
- IdHAL : cecile-neuveglise
- ORCID : 0000-0001-5017-7830
- IdRef : 185868169
Julie Poulain
- Function : Author
- PersonId : 756903
- IdHAL : julie-poulain
- ORCID : 0000-0002-8744-3116
- IdRef : 061407232
Hadi Quesneville
- Function : Author
- PersonId : 736048
- IdHAL : hadi-quesneville
- ORCID : 0000-0003-3001-4908
- IdRef : 137542860
Julia Schumacher
- Function : Author
- PersonId : 771891
- ORCID : 0000-0001-6509-7315
Béatrice Segurens
- Function : Author
- PersonId : 908637
Marc-Henri Lebrun
- Function : Author
- PersonId : 1139104
- ORCID : 0000-0003-1562-1902
- IdRef : 030015995
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
| Origin | Publication funded by an institution |
|---|
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