La protéogénomique pour explorer la biodiversité des organismes non-modèle

International audienceAdvances in next-generation genome sequencing on one hand and high-throughput tandem mass spectrometry on the other have made proteomic experiments applicable to a vast range of organisms. Proteogenomics enables ambitious molecular studies starting from a genome draft or RNAseq data for establishing an exhaustive protein sequence database at a reasonable cost. While the proteomic methodologies are rather standard in these discovery-oriented experiments, interpretation of tandem mass spectrometry raw data remains difficult till now due to the size of the database to be considered and the quality of DNA sequencing and assembling which is far to be as confident as desirable. Besides, the confidence in functional annotation of new key proteins discovered in such experiments is directly linked to the density of closely-related species which have been sequenced and annotated so far. These general points will be exemplified with recent works done on extremophiles, such as the green algae Coccomyxa actinabiotis, and animals, such as the fresh water amphipode Gammarus fossarum. The latter cannot be cultivated as stable isolated specie in controlled laboratory conditions and thus, proteogenomic approaches are really challenging for such sample. Despite these difficulties, the biological impact of different xenobiotics on testis of G. fossarum males could be monitored by high-throughput proteomics. We could also define the core-proteome of the female reproductive organ and explore its conservation throughout different Gammarids. The large molecular biodiversity of Life on Earth is another level of complexity, but as shown with Gammarids, comparative proteogenomics could become more preeminent in evolutionary biology