Dr Marco Galardini, Postodctoral Fellow, European Bioinformatics Institute (EMBL-EBI), will present a lecture entitled: Making sense of genetic diversity: genotype-to-phenotype analysis in an Escherichia coli strain panel

Host : Andrew Page

Abstract:
Understanding how genetic variants, across individuals of the same species, contribute to variability in phenotypes is a central question in genetics. Despite having models that can describe how genetic variability impacts on different molecular layers (e.g. protein stability and function) and statistical association methods, how the ensemble of these effects manifests to cellular phenotypes is still an open question.

To address this problem, we collected a panel of ~1000 Escherichia coli strains  that were genotyped and phenotyped across ~200 growth conditions in order to develop and test predictive phenotypic models. Previous knowledge of E. coli K12 gene function was combined with genome-wide prediction of the impact of genetic variants to predict the growth of ~700 fully sequenced strains. We observed that deleterious mutations in conditionally important genes in E. coli K12 are often but not always associated with poor growth in the respective condition in other strains. This suggests that conditional essentiality is not strictly conserved across strains (e.g. because of epistatic interactions). We also observed that both non-synonymous substitutions and gene content variability have the same importance in determining the phenotype, highlighting the importance of recombination in bacteria.

Lastly, current and future applications of the E. coli strain collection will be presented, demonstrating its potential use as a “community playground” for genotype-to-phenotype studies in bacteria.

All staff from organisations on the Norwich Research Park are welcome to attend.