Josefa Gonzalez

Josefa Gonzalez 

Institute of Evolutionary Biology, Barcelona.

vendredi 31 janvier 2020 - 11h30 Grand salle réunion du CEFE

Transposable elements are ubiquitous, abundant, and active components of genomes. Although most of the mutations caused by transposable elements are likely deleterious or neutral, adaptive mutations have also been repeatedly identified across species. Drosophila melanogaster is an excellent species to quantify the role of transposable elements in environmental adaptation as it has recently colonized very distinct habitats. We have generated 32 D. melanogaster reference genomes using long-read sequencing of flies collected in arid, cold, and temperate environments. The in depth annotation of these genomes has allowed us to discover three new transposable element families in this well-studied species. We have also generated RNA-seq data for 25 of these genomes to investigate the role of transposable elements in expression quantitative trait loci variation and more specifically in desiccation, oxidative, and heavy-metal stress resistance. Our results will allow us to quantify the role of transposable elements in environmental adaptation and to generate testable hypothesis for follow-up functional validation studies.

Recent publications:

1 Rech, G.E. et al Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics, 15(2): e1007900, 2019.

2 Villanueva-Cañas et al. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in D. melanogaster. Nuc Acids Res, 47 (13): 6842–6857 2019

3 Bogaerts-Márquez, M. T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz727. 2019

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Ville Friman

Ville Friman

Department of Biology, University of York, UK

vendredi 24 janvier 2020 - 11h30 Grand salle réunion du CEFE

Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and this this is mainly because the underlying ecology and evolution phage-bacteria interactions are poorly understood in natural rhizosphere microbiomes1,2. We used a combination of field sampling studies, experimental evolution and greenhouse experiments to study ecological and evolutionary dynamics between Ralstonia solanacearum plant pathogenic bacterium and its phage parasites. Our results suggest that phages could be used as a precision tool to engineer the composition of rhizosphere microbiomes by selectively targeting pathogens. Furthermore, phage resistance evolution might not be a problem for the long-term efficiency if we use phages that impose strong evolutionary trade-offs to the pathogen.

Recent publications:

Wang, X., Wei, Z., Li, M., Wang, X., Shan, A., Mei, X., Jousset, A., Shen, Q., Xu, Y. and Friman, V.P., 2017. Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade‐offs. Evolution, 71(3), pp.733-746.

Wang, X., Wei, Z., Yang, K., Wang, J., Jousset, A., Xu, Y., Shen, Q. & Friman, V-P. (2019). Phage combination therapies for bacterial wilt disease in tomato. Nature Biotechnology 37: 1513-1520.

Wei, Z., Gu, Y., Friman, V.P., Kowalchuk, G.A., Xu, Y., Shen, Q. and Jousset, A., 2019. Initial soil microbiome composition and functioning predetermine future plant health. Science Advances, 5(9), p.eaaw0759.

 

Contact : Emanuel Fronhofer

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