# Genome-wide analysis of Corynespora cassiicola putative effectors involved in the CLF disease of rubber tree.

David Lopez, Philippe Label, Boris Fumanal, Sébastien Ribeiro, Annegret

Kohler, R. Ohm, J. Spatafora, I. Grigoriev, Francis Martin, Valérie

Pujade-Renaud

► To cite this version:

David Lopez, Philippe Label, Boris Fumanal, Sébastien Ribeiro, Annegret Kohler, et al.. Genome-wide analysis of Corynespora cassiicola putative effectors involved in the CLF disease of rubber tree.. 12th EFPP-10th SFP conference: Deepen Knowledge in Plant Pathology for Innovative Agro-Ecology, May 2017, Dunkerque, France. hal-01603196

HAL Id: hal-01603196

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Submitted on 5 Jun 2020

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

D. Lopez¹, P. Label¹, B.Fumanal¹, S.Ribeiro¹, A. Kohler², R. Ohm³, J. Spatafora⁴, I. Grigoriev³, F. Martin² and V. Pujade-Renaud⁵

¹UMR 547 PIAF, UCA/INRA, F-63000 Clermont-Ferrand, France
²UMR IAM, INRA/Univ. de Lorraine, 54280 Champenoux, France
³US DOE-JGI, Walnut Creek, California, 94598, USA

⁴Oregon State Univ., Corvallis, Oregon 97331, USA
⁵UMR-AGAP, CIRAD/INRA, F-63000 Clermont-Ferrand, France
valerie.pujade-renaud@cirad.fr

**Background:**

*Corynespora cassiicola* is an Ascomycete fungus (Pleosporale order) with a large host range and diverse life styles¹. In rubber tree, it is responsible for the Corynespora Leaf Fall (CLF) disease which causes massive defoliation on susceptible cultivars, thus impairing natural rubber production²⁻⁶. Genomic and transcriptomic analyses were conducted in order to identify all potential effectors involved in CLF.

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## 1. Interspecies analysis of all putative effectors. Genomes sequences by DOE-JGI ("1000 genomes project")

<figure><img src="image_3.png" /><figcaption>Phylogeny based on 651 concatenated core protein sequences</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>**Fig. 1:** Interspecific phylogeny, protein clustering and putative effectors of 45 fungal species</figcaption></figure>

<figure><img src="image_5.png" /><figcaption>**Fig. 2:** Principal Component Analysis (PCA) based on the composition in all putative effectors from the 45 fungal species.</figcaption></figure>

**Result 1**

* CCP genome is expanded in putative effectors

* Effector-based PCA is only weakly related to phylogeny

* CCP was clustered with two *Colletotrichum sp.*, *F. oxysporum*, *N. hematococca* and *B. dothidea*, in coherency with life style (large host range and multiple trophic modes).

## 2. RNAseq of CCP compatible interaction with rubber tree

<figure><img src="image_6.png" /><figcaption>**CAZymes (52)**</figcaption></figure>

<figure><img src="image_7.png" /><figcaption>**Lipases - Proteases and other secreted proteins (40)**</figcaption></figure>

<caption>**Fig. 3:** Heat map of CCP putative effectors differentially expressed 24 and 48 h after inoculation of detached rubber tree leaves. (*) Genes with predicted secretion signal.</caption>

<caption>**Result 2:** 353 genes were differentially expressed among which 92 putative effectors (52 CAZymes; 40 lipases/peptidases/other secreted proteins; 0 secondary metabolism), including 45 potentially secreted.</caption>

## 3. Intraspecific comparative genomics

<figure><img src="image_8.png" /><figcaption>**Fig. 4:** Intraspecific phylogeny (left) and effector-based PCA (right) of 37 *C. cassiicola* isolates. Phylogeny based on 12 112 concatenated core protein sequences. PCA based on the composition in accessory effectors (612)</figcaption></figure>

<figure><img src="image_9.png" /><figcaption>**PCA of intraspecific diversity of Effectors**</figcaption></figure>

**Result 3:**

Intraspecific effector-PCA based is coherent with the genome-wide phylogeny.

**Conclusion:**

* We have identified *C. cassiicola* (CCP) putative effectors, and more specifically those modulated during its compatible interaction with rubber tree.

* Our comparison of all effectors in phylogenetically diverse *C. cassiicola* isolates will help understanding virulence mechanisms and may provide tools for effector-based selection of more tolerant cultivars⁷.

**References:**

1. SCHOCH, CL (2009), Studies in Mycology;64(1):1-15
2. BRETON, F. (2000), J Rubber Res. 3(2):115-28
3. BARTHE, P. (2007), J Mol. Biol. 367(1):89-101
4. DE LAMOTTE, F. (2007), J Chrom. B: 849(1-2):357-62
5. DÉON, M. (2012), Plant Science. 2012;185-186:227-37
6. DÉON, M. (2014), Fungal Biology. 118(1):32-47
7. TRAN, D.M. (2016), PLoS ONE;11(10)

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cirad

LA RECHERCHE AGRONOMIQUE
POUR LE DÉVELOPPEMENT

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Institut Français
du Caoutchouc

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JOINT GENOME INSTITUTE
DEPARTMENT OF ENERGY