De novo prediction and characterization of the mobilome of Lactobacillales.

Mobile genetic elements (MGEs) are genetic elements that can move within or between DNA molecules or cells. These elements, which include conjugative plasmids and prophages, are one of the main drivers of the genome plasticity that we observe in bacteria and archaea. In addition, they are important for the medical world (e.g. as spreaders of antimicrobial resistance) and biotechnology industry (as a source of genetic engineering tools). Therefore, it is highly useful to be able to computationally detect the presence of MGEs in prokaroytic genomes, as well as predict to which strains an MGE can potentially transfer (its host range). However, current techniques for the former are limited because they are dependent on databases of experimentally characterized MGEs, while current host range prediction strategies are very coarse-grained. In this project, a computational tool will be developed that is capable of predicting MGEs in prokaroytic genomes in a databaseindependent way. The tool will achieve this by taking as input a multigenome, multi-species dataset instead of a single genome, and adopting a comparative genomics approach. In addition, a novel strategy for high-resolution host range prediction will be developed, based on comparative phylogenomics and host strain gene content. Both novel techniques, as well as existing tools, will be used to predict and characterize the comprehensive "mobilome" of the medically and economically important order Lactobacillales.

Keywords:GENOMICS, LACTOBACILLUS, EVOLUTION, BIOINFORMATICS

Disciplines:Molecular evolution, Phylogeny and comparative analysis, Bacteriology, Computational evolutionary biology, comparative genomics and population genomics, Development of bioinformatics software, tools and databases