PhD project – Transposable elements of rust fungi genomes

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PhD project – Transposable elements of rust fungi genomes

Background. Fungi of the order Pucciniales cause rust diseases on many plants including major crops in Agriculture. In the past decades, a dozen rust fungi genomes have been sequenced by international consortia in collaboration with international sequencing centers. Rust fungi genomes are very large (up-to >1 Gb) and they exhibit large numbers of predicted genes compared to other fungi (see Aime et al. 2017; Petre & Duplessis, 2022). Repeat elements account for 40 to > 90 % of rust genomes and transposable elements are responsible for the observed genome inflation.

Aim: We propose to perform a comparative genomic analysis of transposable elements (TE) in rust fungi genomes considering different levels of comparison from genera to taxonomical family and order levels, and beyond with the subphylum Pucciniomycotina to which the order Pucciniales belongs. The aim is to study how these TE expanded in rust genomes and how they did shape the rust genomic landscape through evolution and how they influenced diversification of expanded gene families (e.g. genes involved in life cycle transitions, effectors).

We are looking for an enthusiastic student with skills in bioinformatics who is motivated to perform comparative analysis of TE in rust fungi genomes. The PhD project is bioinformatic-oriented on data already acquired and does not contain experimental wet lab, although it may be considered depending on the candidate’s interest (more details can be shared). The project will be set in connection with international collaborators, and locally, in relative autonomy, with the support of a small team of skilled bioinformaticians.

The hosting team is about 40 people working on ecology and biology of mycorrhizal and pathogenic fungi as well as tree-interacting and soil bacteria. Several comparative genomic projects are ongoing on different model organisms. The team hosts PhDs, postdocs and invited researchers from different countries, making a stimulating environment to develop a fruitful PhD  project. The successful candidate will work more closely with INRAE researchers in the frame of an interdisciplinary project focused on mechanisms and evolution of host-rust interactions.

Requirements: Skills in bioinformatics / genomics incl. basic/advanced skills in Python and/or R. Being organized and with the capacity to work in relative autonomy. Spoken and written english.

Contact: Sebastien Duplessis


Twitter: @SebbyRust



How to apply: Applicants should submit a complete application package by e-mail to the contact provided below.

The application package should contain: 1) a curriculum vitae; 2) a copy of the Master degree with details of marks and ranks obtained in the Master degree; 3) a letter detailing motivations; how skills from initial training at university make this application sound to this PhD proposal; and what is the project of the applicant after the PhD; and 4) name, address, phone number and email of at least two references (internship experience or university training)

IMPORTANT: please indicate [PhD APPLICATION] as email title


Contract: PhD student (paid by INRAE)

Duration: 36 months

Beginning: October 1st or November 1st, 2022

Remuneration: ~20K€/year (net of charge); complementary income possible through teaching at university.

Doctoral school: SIReNa

Deadline of application: August 31st, 2022

INRAE Center: Grand Est Nancy (F-54280 Champenoux, France)

Research department: UMR 1136 IAM

INRAE/Université de Lorraine – Tree-Microbe Interactions


Related reading:

  • Aime MC, McTaggart AR, Mondo SJ, Duplessis S (2017) Phylogenetics and phylogenomics of rust fungi. In: Fungal phylogenetics and phylogenomics. Townsend JP & Wang Z, Eds. Elsevier Academic Press, Cambridge, MA, USA. Advances in Genetics Vol 100: 267-307.
  • Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC (2021) Host adaptation and virulence in heteroecious rust fungi. Annual Review of Phytopathology. 59: 403-422. doi: 10.1146/annurev-phyto-020620-121149
  • Lorrain C, Goncalves Dos Santos KC, Germain H, Hecker A, Duplessis S (2019) Advances in understanding obligate biotrophy in rust fungi. Tansley review, New Phytologist. doi: 10.1111/nph.15641.
  • Gupta,YK, Marcelino-Guimarães FC, Lorrain C, Farmer AD, Haridas S, et al. (2022) The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes. Archive available on BioRxiv:
  • Petre B, Duplessis S (2022) A decade after the first Pucciniales genomes – a snapshot of (post) genomics studies in three model rust fungi. Archive available on HAL at


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