"The project proposed for the IEF concerns Mycobacterium avium subsp paratuberculosis (Map) which causes Johne’s disease (JD), a chronic gastroenteritis affecting principally ruminants and responsible for significant global economic losses to the livestock and associated industries. Controversially, Map has been associated with Crohn’s disease in humans. The epidemiology of paratuberculosis is poorly understood and there is little information on the virulence of strain types, interspecies transmission or wildlife reservoirs. The project will analyse genome sequences from 100 Map isolates to study genetic diversity and evolution. An understanding of the evolutionary dynamics of Map populations has important implications for the control of JD and genome information can provide insights into virulence, pathogenicity and host preference. The objectives are to assemble and annotate the genome sequence of a Type I Map strain, to identify single nucleotide polymorphisms that can discriminate the different strain types, human and pigmented isolates and to perform phylogenetic analysis. Few whole genome intraspecies comparisons of pathogenic bacteria have been done on this scale and this will be the first of such studies in mycobacteria. The project employs state-of-the-art technologies for genome sequencing and analyses and has a European dimension. The fellow will acquire crucial new bioinformatics skills and transferable skills that complement her current knowledge and experience to progress her chosen career in the field of evolutionary biology and diversification of pathogens. This will give her a competitive advantage for a senior research position and will promote networking of scientists across Europe, thereby contributing to the European Research Area."