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Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

Abstract

Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum,more » Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, and Botrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms.« less

Authors:
 [1];  [2];  [1];  [1];  [1];  [3];  [4];  [5];  [5];  [5];  [5];  [6];  [5];  [7];  [8];  [9];  [2]
+ Show Author Affiliations
  1. Univ. Clermont Auvergne, Clermont-Ferrand (France)
  2. Univ. Clermont Auvergne, Clermont-Ferrand (France); CIRAD, UMR AGAP, Clermont-Ferrand (France); Univ. Montpellier, Montpellier (France)
  3. UMR INRA-Univ. de Lorraine “Interaction Arbres/Microorganismes,” Champenoux (France)
  4. Univ. Estadual de Maringá, Maringá (Brazil)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Utrecht Univ., Utrecht (Netherlands)
  7. Oregon State Univ., Corvallis, OR (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  9. Université de Lorraine, Champenoux (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Laboratory of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems (ARBRE)
OSTI Identifier:
1544038
Alternate Identifier(s):
OSTI ID: 1619090
Grant/Contract Number:  
AC02-05CH11231; ANR-11-LABX-0002-01
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbiology; Corynespora cassiicola; Hevea brasiliensis; plant-pathogens interaction; effectors; cassiicolin; genomics; gene expression

Citation Formats

Lopez, David, Ribeiro, Sébastien, Label, Philippe, Fumanal, Boris, Venisse, Jean -Stéphane, Kohler, Annegret, de Oliveira, Ricardo R., Labutti, Kurt, Lipzen, Anna, Lail, Kathleen, Bauer, Diane, Ohm, Robin A., Barry, Kerrie W., Spatafora, Joseph, Grigoriev, Igor V., Martin, Francis M., and Pujade-Renaud, Valérie. Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. United States: N. p., 2018. Web. doi:10.3389/fmicb.2018.00276.
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Lopez, David, Ribeiro, Sébastien, Label, Philippe, Fumanal, Boris, Venisse, Jean -Stéphane, Kohler, Annegret, de Oliveira, Ricardo R., Labutti, Kurt, Lipzen, Anna, Lail, Kathleen, Bauer, Diane, Ohm, Robin A., Barry, Kerrie W., Spatafora, Joseph, Grigoriev, Igor V., Martin, Francis M., & Pujade-Renaud, Valérie. Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. United States. https://doi.org/10.3389/fmicb.2018.00276
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Lopez, David, Ribeiro, Sébastien, Label, Philippe, Fumanal, Boris, Venisse, Jean -Stéphane, Kohler, Annegret, de Oliveira, Ricardo R., Labutti, Kurt, Lipzen, Anna, Lail, Kathleen, Bauer, Diane, Ohm, Robin A., Barry, Kerrie W., Spatafora, Joseph, Grigoriev, Igor V., Martin, Francis M., and Pujade-Renaud, Valérie. Fri . "Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors". United States. https://doi.org/10.3389/fmicb.2018.00276. https://www.osti.gov/servlets/purl/1544038.
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@article{osti_1544038,
title = {Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors},
author = {Lopez, David and Ribeiro, Sébastien and Label, Philippe and Fumanal, Boris and Venisse, Jean -Stéphane and Kohler, Annegret and de Oliveira, Ricardo R. and Labutti, Kurt and Lipzen, Anna and Lail, Kathleen and Bauer, Diane and Ohm, Robin A. and Barry, Kerrie W. and Spatafora, Joseph and Grigoriev, Igor V. and Martin, Francis M. and Pujade-Renaud, Valérie},
abstractNote = {Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, and Botrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms.},
doi = {10.3389/fmicb.2018.00276},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {United States},
year = {Fri Mar 02 00:00:00 EST 2018},
month = {Fri Mar 02 00:00:00 EST 2018}
}
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https://doi.org/10.3389/fmicb.2018.00276
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Cited by: 39 works
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Figures / Tables:

TABLE 1 TABLE 1: (A) Metrics of the CCP genome assembly (B) Repetitive DNA content and transposable elements.
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