Pan Genome Analysis

Pan Genome Analysis

Overview: 

Pan-genomic analysis leverages recent advances in the ability to routinely sequence and annotate whole genomes. No longer restricted to considering one genome at a time, the capability now exists to study multiple genomes from the same taxonomic grouping and observe how genomes change with evolutionary time and with adaptations to new environmental niches. It is possible, for example, to trace the evolution of a single enzyme as structure changes to fit function. However, the role of any genes in living systems is highly pleiotropic, its function dependent upon the interactions and regulation of many other genes. Through pan-genomic analysis we have identified that a microorganism’s characteristics is not well predicted by any individual gene or gene function, rather a microorganism’s role is best predicted as an emergent property of its genome, i.e. its metabolome and its transportome. Our unique computational approach to modeling a microorganism’s transportome, PRTT, has proven to be most predictive of a microorganism’s function. This insight had provided specific motivation for protein production and functional characterization. Pan-genomic Analysis leverages previously sequenced annotated microorganism genomes to identify, not only specific gene functions, but also interacting gene networks that are associated with desired biological functions, such as the capacity to consume specific carbon sources. Unique capacity to model secondary metabolome and transportome lead to unique, non-central metabolism targets for genomic manipulation. Pan-genomic Analysis is limited only by the number of available genomes and the knowledge of microorganisms’ native habitats.

References and Additional Information: 

PE Larsen, FR Collart, Y Dai (2015). Predicting ecological roles in the rhizosphere using metabolome and transportome modeling. PloS one 10 (9), e0132837.

Peter E Larsen, Frank R Collart, Yang Dai (2014). Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections. Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE.

S Shinde, JR Cumming, FR Collart, PH Noirot, PE Larsen (2017). Pseudomonas fluorescens transportome is linked to strain-specific plant growth promotion in Aspen seedlings under nutrient stress. Frontiers in plant science 8, 348.

Labs:

Argonne National Laboratory

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