Damien Courtine (CIML - I2M)
Global and local genome sequence analysis to understand fungal virulence
Team: Jonathan Ewbank (CIML) - Laurent Tichit (I2M) - Guillaume Blanc (MIO)
April 2019 - present | CENTURI postdoctoral fellow
2014 - 2018 | PhD, Microbiology- University of Western Brittany (Brest, France)
2014 | MSc degree in Bioinformatics- Blaise Pascal University (Clermont-Ferrand, France)
About his postdoctoral project
Interaction between C. elegans and its natural pathogen Drechmeria coniospora, using a Swedish isolate of the fungus. After 20 years of serial passage in C. elegans, the strain has evolved to become more virulent. A separate Danish strain is even more virulent. A superficial comparison of their genomes indicates high local sequence similarity, but surprisingly extensive genome rearrangement (Lebrigand et al. PLoS Genetics, 2016). We plan to use ONT nanopore sequencing to establish the extent of this unexpected genome plasticity across several Drechmeria strains and its link with virulence. ONT sequencing suffers from miscalling of homopolymer sequences, rendering local comparison problematic. New algorithms are needed to deal with this problem, to allow ONT-only comparative genomics.