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Background:

The ascomycete Leveillula taurica causes powdery mildew of pepper, resulting in
yield losses of up to 40%. This obligate biotrophic fungus has a wide host range including different
plant families such as Solanaceae, Asteraceae and Cucurbitaceae. Molecular diversity studies of
this pathogen, mainly based on the ITS (internal transcribed spacer), have revealed different
clades distributed by host species (Khodaparast et al. 2012). This pathogen is present at a
worldwide level on pepper crop, however the L. taurica diversity isolated on pepper crops have
never been conducted, neither phenotypically, nor molecularly. Despite the importance of this
pathogen, very few molecular information exists. Recently, a draft genome has been published
(Kush et al. 2020), but no reference genome is available yet. Studying the diversity of this pathogen
could help breeding strategies for durable resistant pepper varieties.

Goals:

The aim of the internship it to study the diversity of the pathogen Leveillula taurica, using
both phenotypic and molecular characterizations. The calendar will be adapted depending on the
trainee level and period of internship.

Strategies

Task 1 - Phenotypic characterization: A collection of 100 isolates have been obtained from
different countries, a diversity of fields, and on different pepper varieties. The aim will be to collect
a relevant number of spore images by microscopy on this collection. Analysis of the images, using
ImageJ software, will permit to collect phenotyping measurements regarding the shape of the
spores (length, width, aspect). The phenotypic database obtained will be analyzed thanks to
statistical analyses. We aim at determining whether there is a structuration of the diversity of L.
taurica based on their phenotypical information, and/or according to the host of origin or the
geographical origin of the isolate.

Task 2 - Molecular characterization: The draft genome available in literature does not allow to
conduct a diversity study as it is fragmented and rely on a single isolate. Currently we are
developing a high weight DNA extraction method to perform long-read sequencing. We plan to
have a new genome assembly before the internship. Short read sequencing on few isolates is also
plan ahead of the training. This sequencing will permit to develop a SNP (single nucleotide
polymorphism) matrix to develop a method to genotype targets on our whole L. taurica collection.
The student will assist in the DNA extraction of the 70 remaining isolates, for the genotyping based
on the sequencing previously obtained. The student will use the results obtained to conduct a
genetic distance analysis, build a phylogenetic tree, but also investigate the admixture of the L.
taurica samples. He/She will also use the sequencing information obtained to explore some key
genes in other fungi species, such as virulence effectors, or the MAT (mating type) locus, known
to have an important role in the fungi population structuration.
Overall, the phenotypic, molecular, and the metadata will be combined as one dataset to conclude
on the population structuration of the collection.

References

Khodaparast, S. A., Takamatsu, S., Harada, M., Abbasi, M., & Samadi, S. (2012). Additional rDNA ITS
sequences and its phylogenetic consequences for the genus Leveillula with emphasis on conidium
morphology. Mycological Progress, 11(3), 741–752. https://doi.org/10.1007/s11557-011-0785-7

Kusch, S.; Németh, M. Z.; Vaghefi, N.; Ibrahim, H. M. M.; Panstruga, R.; Kiss, L. (2020): A Short-Read
Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper
(Capsicum annuum). Molecular Plant-Microbe Interactions, 33 (6), pp. 782–786. DOI: 10.1094/MPMI-
02-20-0029-A.

Prerequisites

Hard skills: general interest in molecular biology and in microscopy, basis experience in R
software and in statistics, reading scientific articles in English.

Soft skills: motivation, curiosity, a major investment
 

Application: send your application to flavie.cussonneau@inrae.fr and
veronique.lefebvre@inrae.fr, enclosing your CV, a one-page covering letter, your grades from the
previous academic year and the first semester of this year.

Selection: on the basis of the application, followed by an interview with pre-selected candidates
at INRAE GAFL or by videoconference.

Supervisors: Flavie Cussonneau (PhD Student) & Véronique Lefebvre (Team leader)