Mots-Clés

Elements transposables Transcriptomique Domestication Virus

Description

Context:

Research unit:

Currently counting over 150 staff members including non-permanent personnel, UMR 1332 BFP is a partnership between INRAE (Divisions of Biology and Plant Breeding and Plant Health and Environment) and the University of Bordeaux. It constitutes a major pillar of plant biology research in Nouvelle- Aquitaine.
You will join the Virology team, and you will be supervised by Quynh Trang-Bui and Marie Lefebvre.

Scientific:

Transposable elements (TEs) are major components of eukaryotic genomes and can constitute up to 80% of the plant genomes. McClintock originally identified TEs in the 1940’s, she referred to them as ‘Controlling elements’ based on their fundamental characteristics of gene expression regulation. Therefore, many experimental evidences indicate that TEs can play key regulatory roles in controlling the gene expression during plant development and stress responses in various ways. TEs can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. Studying the distribution of TEs in host genome and their expression profiles will help to determine the role of TEs in many layers of gene expression regulation as well as their contribution to the plasticity of host genomes and the evolution/ adaptation of species.

Apricots (Prunus armeniaca species) are stone fruit trees, which are some of the most important dietary crops worldwide, underpinning many local economies in lower-income countries. This species presents a striking interest, since it is extensively available both as domesticated and wild forms. However, as for other tree species, Prunus fruit tree breeding programs are continually challenged to find genetic solutions for producing nutritionally-improved varieties while facing dynamic problems of ever-changing abiotic and biotic conditions. Among those challenges, the most critical is the current uncontrolled spread of Plum pox virus (PPV). Moreover, due to its relatively small genome (220 Mbp), apricot is, in our hands, a model plant for understanding evolutionary and genomic processes associated with domestication and plant adaptation of an important fruiting crop species. In the frame of our GEP4TWAS project (Gene Expression Profiling for Transcriptome-Wide Association Studies), transcriptomics data are available for cultivated and wild apricots as well as three bulks of wild susceptible and resistant accessions.

Aims of internship:

As described above, transposable elements can regulate and affect gene expression not only due to their moving capacity within the genome but also because of its transcriptional activity. The aim of internship work is to respond to these questions: 1) what is the TE distribution in apricot genome and its interaction with genome organization? 2) what are the effects of domestication and virus infection on plant TE activity?

Schedule:

1. First objective: reveal the distribution of TEs and its relationship with host genes in apricot genomes. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes: https://github.com/marieBvr/TEs_genes_relationship_pipeline. The trainee will analyze the results available from this pipeline (big data in csv) to report the distribution of TEs in P. armeniaca genome (Marouch #14).
2. Second objective: detect TE expression profiles in cultivated/wild apricots as well as in PPV resistant/susceptible wild apricots. The TE expression profiles will be detected and compared between wild and cultivated apricots as well as between PPV infected, susceptible and resistant wild apricot (P. armeniaca transcriptomics data available from the GEP4TWAS project). This TE differential expression analysis will be performed with SQuIRE tool. This work will allow clarifying the role of TEs in genome evolution and providing novel insights into the function of mobile elements at the core of regulatory networks. More interestingly, these research directions in domestication and disease resistance will further our understanding of the interaction between TEs and host genomes in responses to environmental challenges.

Profil:

Bioinformatics analyst (and not developers/programmers) or Biologist who is familiar with Linux/R and motivated to develop competences in Bio-analysis.

Références:

Groppi, A., Liu, S., Cornille, A. et al. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun 12, 3956 (2021). DOI: 10.1038/s41467-021-24283-6.

Kong, Y., Rose, C. M., Cass, A. A., Williams, A. G., Darwish, M., et al. 2019. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nature Communications, 10(1): 5228.

Lanciano, S., & Cristofari, G. 2020. Measuring and interpreting transposable element expression. Nature Reviews Genetics, 21(12): 721–736.

Wells, J. N., & Feschotte, C. 2020. A Field Guide to Eukaryotic Transposable Elements. Annual Review of Genetics, 54(1): 539–561.

Yang, W. R., Ardeljan, D., Pacyna, C. N., Payer, L. M., & Burns, K. H. 2019. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Research, 47(5): e27–e27.