The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
Pierre J. G. M. de Wit
(1, 2)
,
Ate van Der Burgt
(1, 3)
,
Bilal Okmen
(1)
,
Ioannis Stergiopoulos
(1, 2, 4)
,
Kamel A. Abd-Elsalam
(5)
,
Andrea L. Aerts
(6)
,
Ali H. Bahkali
(7)
,
Henriek G. Beenen
(1)
,
Pranav Chettri
,
Murray P. Cox
,
Erwin Datema
,
Ronald P. de Vries
,
Braham Dhillon
,
Austen R. Ganley
,
Scott A. Griffiths
(1)
,
Yanan Guo
,
Richard C. Hamelin
,
Bernard Henrissat
(8)
,
M. Shahjahan Kabir
,
Mansoor Karimi Jashni
(1)
,
Gert Kema
,
Sylvia Klaubauf
,
Alla Lapidus
(6)
,
Anthony Levasseur
(9)
,
Erika Lindquist
(6)
,
Rahim Mehrabi
(1)
,
Robin A. Ohm
(6)
,
Timothy J. Owen
,
Asaf Salamov
(6)
,
Arne Schwelm
,
Elio Schijlen
,
Hui Sun
(6)
,
Harrold A. van den Burg
(1, 2)
,
Roeland C. H. J. van Ham
,
Shuguang Zhang
,
Stephen B. Goodwin
,
Igor V. Grigoriev
(6)
,
Jerome Collemare
(1, 2)
,
Rosie E. Bradshaw
Ioannis Stergiopoulos
- Fonction : Auteur
- PersonId : 776760
- ORCID : 0000-0002-2368-6119
Pranav Chettri
- Fonction : Auteur
Murray P. Cox
- Fonction : Auteur
Erwin Datema
- Fonction : Auteur
Ronald P. de Vries
- Fonction : Auteur
Braham Dhillon
- Fonction : Auteur
Austen R. Ganley
- Fonction : Auteur
Yanan Guo
- Fonction : Auteur
Richard C. Hamelin
- Fonction : Auteur
Bernard Henrissat
- Fonction : Auteur
- PersonId : 833340
M. Shahjahan Kabir
- Fonction : Auteur
Gert Kema
- Fonction : Auteur
Sylvia Klaubauf
- Fonction : Auteur
Timothy J. Owen
- Fonction : Auteur
Arne Schwelm
- Fonction : Auteur
Elio Schijlen
- Fonction : Auteur
Roeland C. H. J. van Ham
- Fonction : Auteur
Shuguang Zhang
- Fonction : Auteur
Stephen B. Goodwin
- Fonction : Auteur
Rosie E. Bradshaw
- Fonction : Auteur
Résumé
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an alpha-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.
Mots clés
Domaines
Sciences du Vivant [q-bio]Format du dépôt | Fichier |
---|---|
Type de dépôt | Article dans une revue |
Titre |
en
The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
|
Résumé |
en
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an alpha-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.
|
Auteur(s) |
Pierre J. G. M. de Wit
1, 2
, Ate van Der Burgt
1, 3
, Bilal Okmen
1
, Ioannis Stergiopoulos
1, 2, 4
, Kamel A. Abd-Elsalam
5
, Andrea L. Aerts
6
, Ali H. Bahkali
7
, Henriek G. Beenen
1
, Pranav Chettri
, Murray P. Cox
, Erwin Datema
, Ronald P. de Vries
, Braham Dhillon
, Austen R. Ganley
, Scott A. Griffiths
1
, Yanan Guo
, Richard C. Hamelin
, Bernard Henrissat
8
, M. Shahjahan Kabir
, Mansoor Karimi Jashni
1
, Gert Kema
, Sylvia Klaubauf
, Alla Lapidus
6
, Anthony Levasseur
9
, Erika Lindquist
6
, Rahim Mehrabi
1
, Robin A. Ohm
6
, Timothy J. Owen
, Asaf Salamov
6
, Arne Schwelm
, Elio Schijlen
, Hui Sun
6
, Harrold A. van den Burg
1, 2
, Roeland C. H. J. van Ham
, Shuguang Zhang
, Stephen B. Goodwin
, Igor V. Grigoriev
6
, Jerome Collemare
1, 2
, Rosie E. Bradshaw
1
Phytopathol Lab
( 448475 )
- Pays-Bas
2
Ctr BioSyst Genom
( 448476 )
- Pays-Bas
3
Lab Bioinformat
( 448477 )
- Pays-Bas
4
Dept Plant Pathol
( 262027 )
- Davis
- États-Unis
5
Agr Res Ctr
( 448479 )
- Égypte
6
Joint Genome Inst
( 448480 )
- États-Unis
7
KSU -
King Saud University [Riyadh]
( 302265 )
- King Saud University, Riyadh 12372
- Arabie saoudite
8
AFMB -
Architecture et fonction des macromolécules biologiques
( 199349 )
- Faculté des Sciences de Luminy - ESIL 163 avenue de Luminy CP 925 13288 MARSEILLE CEDEX 09
- France
9
BBF -
Biodiversité et Biotechnologie Fongiques
( 37914 )
- Faculté des Sciences de Luminy - ESIL 163 avenue de Luminy CP 925 13288 MARSEILLE CEDEX 09
- France
|
Public visé |
Scientifique
|
Numéro d'article |
|
Version du document |
version éditeur
|
Licence |
Paternité
|
Langue du document |
Anglais
|
Nom de la revue |
|
Vulgarisation |
Non
|
Comité de lecture |
Oui
|
Audience |
Non spécifiée
|
Date de publication |
2012
|
Volume |
8
|
Numéro |
11
|
Page/Identifiant |
np
|
Domaine(s) |
|
Financement |
|
Projet(s) Européen(s) |
|
Mots-clés |
en
INDUCED POINT MUTATION, FUSIFORM RUST DISEASE, AVIRULENCE GENE AVR9, MATING-TYPE GENES, ASPERGILLUS-NIDULANS, NEEDLE BLIGHT, LEPTOSPHAERIA-MACULANS, FOREST PATHOGEN, LEAF MOLD, CELL-WALL, Fungi, Fungal genetics, Fungal genomics, Tomatoes, Plant fungal pathogens, Gene expression, Genome analysis, Gene prediction
|
DOI | 10.1371/journal.pgen.1003088 |
ProdINRA | 212764 |
Pubmed Id | 23209441 |
UT key WOS | 000311891600067 |
Origine :
Publication financée par une institution
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