Bioinformatic: Python, Bash, R, JAVA programming. Next Generation Sequencing (NGS) data analysis (transcriptomics, RNA-seq). Molecular phylogeny.
Molecular biology: RNA and DNA extraction, PCR, qPCR.
Key-words: Transcriptomic, metagenomic, non-model animals, new viruses, evolution
My PhD research thematic is the study of non-biased and global viral biodiversity through non-model animals’ transcriptomes. Majority of characterized viruses have as host the Human, domestic and farmed animals, or insects known as disease vector. Interestingly, non-model animals with more than one million of species in the world can therefore be a reservoir of a huge viral diversity that remains to be characterized. The goal of this PhD is thus to study under characterized animals in order to learn more about their virus history.
Metagenomic allows the study the genetic content of complex environment, here marine or terrestrial non-model animal species, which were able to interact with a diversity of known or unknown viruses during evolution. This approach will help us to fill our gaps and understand evolutionary history of these viruses and their hosts.
I currently have a set of 441 transcriptomes, the expressed part of genomes, sequenced by Illumina technology. The aim of my PhD researches is to detect the presence of viruses, either exogenous or endogenous viral elements, within host genomes. Only few virus families are known to integrate host genome and to participate to host genome evolution. This work aims therefore at discover new viruses by the way of bioinformatic analyses of animal transcriptome, of viral genome reconstruction and of phylogenetic tree construction, to replace new viruses within the virus taxonomy and identify their origin.