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

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

doi:10.3389/fmicb.2018.00276

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

Journal Article · Fri Mar 02 00:00:00 EST 2018 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2018.00276· OSTI ID:1544038

Lopez, David ^[1]; Ribeiro, Sébastien ^[2]; Label, Philippe ^[1]; Fumanal, Boris ^[1]; Venisse, Jean -Stéphane ^[1]; Kohler, Annegret ^[3]; de Oliveira, Ricardo R. ^[4]; Labutti, Kurt ^[5]; Lipzen, Anna ^[5]; Lail, Kathleen ^[5]; Bauer, Diane ^[5]; Ohm, Robin A. ^[6]; Barry, Kerrie W. ^[5]; Spatafora, Joseph ^[7]; Grigoriev, Igor V. ^[8]; Martin, Francis M. ^[9]; Pujade-Renaud, Valérie ^[2]

Univ. Clermont Auvergne, Clermont-Ferrand (France)
Univ. Clermont Auvergne, Clermont-Ferrand (France); CIRAD, UMR AGAP, Clermont-Ferrand (France); Univ. Montpellier, Montpellier (France)
UMR INRA-Univ. de Lorraine “Interaction Arbres/Microorganismes,” Champenoux (France)
Univ. Estadual de Maringá, Maringá (Brazil)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Utrecht Univ., Utrecht (Netherlands)
Oregon State Univ., Corvallis, OR (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Université de Lorraine, Champenoux (France)

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.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Laboratory of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems (ARBRE)

Grant/Contract Number:: AC02-05CH11231; ANR-11-LABX-0002-01

OSTI ID:: 1544038

Alternate ID(s):: OSTI ID: 1619090

Journal Information:: Frontiers in Microbiology, Vol. 9; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 39 works

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An updated phylogenetic classification of Corynespora cassiicola isolates and a practical approach to their identification based on the nucleotide polymorphisms at the ga4 and caa5 loci Banguela-Castillo, Alexander; Ramos-González, Pedro L.; Peña-Marey, Mabel Mycologia, Vol. 112, Issue 1 https://doi.org/10.1080/00275514.2019.1670018	journal	November 2019
Effects of early‐season insect herbivory on subsequent pathogen infection and ant abundance on wild cotton ( Gossypium hirsutum ) Abdala‐Roberts, Luis; Pérez Niño, Biiniza; Moreira, Xoaquín Journal of Ecology, Vol. 107, Issue 3 https://doi.org/10.1111/1365-2745.13131	journal	November 2018
Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum Pritam, Manisha; Singh, Garima; Swaroop, Suchit BMC Bioinformatics, Vol. 19, Issue S13 https://doi.org/10.1186/s12859-018-2482-x	journal	February 2019
Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber Gao, Shigang; Zeng, Rong; Xu, Lihui BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-01873-w	journal	July 2020
Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) Ametrano, Claudio G.; Grewe, Felix; Crous, Pedro W. IMA Fungus, Vol. 10, Issue 1 https://doi.org/10.1186/s43008-019-0018-2	journal	October 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Microbiology
Corynespora cassiicola
Hevea brasiliensis
plant-pathogens interaction
effectors
cassiicolin
genomics
gene expression