Microbial genotype-to-phenotype studies in the pangenome era
New Voices in Infection Biology
- Datum: 18.05.2022
- Uhrzeit: 16:00
- Vortragende(r): Marco Galardini
- Twincore, Center for Experimental and Clinical Infection Research, Hannover
- Ort: Zoom video conference
- Gastgeber: Silvia Portugal
- Kontakt: firstname.lastname@example.org
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The advent of relatively inexpensive genome sequencing has brought to light the very high degree by which microbial species can vary in their genetic content, collective termed “pangenome”. These genetic variations are responsible for phenotypes that are relevant for infection, such as niche survival, antimicrobial resistance and interaction with the host. Linking genotype to phenotype is however a challenging task, and is even more complicated in microbial pangenomes due to the scale of the problem and due to the challenge to represent core and accessory genome variation. In this talk I will present statistical genetics approaches to link genotype and phenotype in bacteria and its application to E. coli and P. aeruginosa virulence, as well as some solutions to improve the way associated variants are annotated. Lastly, I will spend a few words on our attempts at improving gene annotation in pangenomes and challenges in scaling up analyses when sample sizes reach 10^6.