Master thesis (internship)

Niveau Master 2 / Recherche

Team Evolution and genomes

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Supervisors Aurelie Hua-Van (ahuavan@egce.cnrs-gif.fr) and Arnaud Le Rouzic (lerouzic@egce.cnrs-gif.fr), in collaboration with Anne Genissel (anne.genissel@inrae.fr, BIOGER Unit, Thiverval-Grignon).

Title Understanding the link between transposable element and transcriptome evolution of the fungal pathogen Zymoseptoria tritici.

Keywords Transposable elements – cis-regulation – transcriptome – experimental evolution – fungi.

Context

Selfish elements can be domesticated by their host genome and play a significant role in adaptive evolution, either by creating new mutations or transposable element-derived coding genes. Transposable elements (TE) also may affect gene expression regulation. There is now growing evidence that TEs can affect gene expression regulation and gene network (see for review Chuong et al., 2017). TEs play an important role in fungal genome evolution (Muszewska et al., 2019). Recent work shows that TEs are involved in rapid adaptation against host resistance in the fungal plant pathogen Zymoseptoria tritici (Singh et al., 2021). We study the fungal pathogen Zymoseptoria tritici, which was fully sequenced in 2011 and TE families have been well described in that species (Goodwin, 2011; Dhillon, 2014). In addition, recent literature highlights strong variation in TE content among natural fungal isolates (Badet et al., 2020, Lorrain et al., 2021). However, the role of TE in gene expression regulation is still unknown in this species.

We recently performed an experimental evolution with the wheat fungal pathogen Zymoseptoria tritici, submitted to stable or fluctuating temperatures for one year in vitro (17ºC, 23ºC or shifts between 17ºC and 23ºC every 2,5 days). One year in our conditions represents at least 500 generations of asexual multiplications. While recent work identified differentially expressed genes under stable or fluctuating selection regimes, and that differentially expressed genes were often located in regions known to be enriched in transposable elements, the fate of transposable elements during this lab evolution is yet unknown (Jallet et al, 2020). We sequenced RNA for 8 out of 18 evolved lineages and their 2 ancestors at 17ºC and 23ºC in duplicates (40 transcriptomes), and we are currently obtaining the genomes of all lineages as well (10 are already analyzed).

Objectives

The main objective of the training is to identify whether TE-mediated mutations occurred during our experimental evolution, and find if TE expression has been changed during the experimental evolution. To reach this goal, we propose a two-tiered approach. First, we will examine the distribution and the nature of TEs, and compare its composition between ancestor and evolved lineages. Can we identify de novo TE insertions? What is the nature of these elements that did transpose during the experimental evolution? Are DEGs nearby active TEs? Next, we will study the variation of TE expression itself (DET: differential expression of TE), based on the findings on TE transposition identified in the first step. Which genomic regions carry DETs? Is there an effect of the selection regime on DETs? What is the interplay between the host gene expression evolution and TE expression evolution?

Good knowledge in evolution and genomics is required. The student will be expected to conduct mostly bioinformatic analyses in order to detect structural variants among the lineages. Using bioinformatic tools on Illumina data for all lineages and minION sequence data for the ancestors, we will annotate TE and seek differences among the genomes. Knowledge in statistics for differential gene expression analysis is a plus.

The training will take place at IDEEV in the EGCE Unit, with Aurelie Hua-Van (ahuavan@egce.cnrs-gif.fr) and Arnaud Le Rouzic (lerouzic@egce.cnrs-gif.fr), in collaboration with Anne Genissel (anne.genissel@inrae.fr, BIOGER Unit, Thiverval-Grignon).

References

Badet, T., Oggenfuss, U., Abraham, L., McDonald BA. and D. Croll. 2020. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria triticiBMC Biol 18, 12 (2020)

Chuong EB., Elde NC, and C Feschotte. 2017. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet 18, 71-86.

Dhillon B, Gill N, Hamelin RC, Goodwin SB. 2014. The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola. BMC Genomics. 15: 1132.

Goodwin, S.B., M’ Barek, S.B., Dhillon, B., Wittenberg, A.H., Crane, C.F., Hane, J.K., et al., 2011. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet. 7, e1002070.

Jallet AJ., Le Rouzic A. and A. Genissel. 2020. Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici. Frontiers in Microbiology, 11: 2180.

Lorrain C., Feurtey A., Möller M., Haueisen J. and E. Stukenbrock. 2021. Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses. G3 11, jkab068.

Muszewska, A., Steczkiewicz, K., Stepniewska-Dziubinska, M. and K. Ginalski. 2019. Transposable elements contribute to fungal genes and impact fungal lifestyle. Sci Rep 9, 4307.

Singh, N.K., Badet, T., Abraham, L. and D. Croll. 2021. Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen. BMC Genomics22,393.