## 3 Genetics  
The genome of _E. amylovora_ consists of a circular chromosome of 3,805,874 bp and two plasmids: AMYP1 (28,243 bp), also reported as PEA29, and the larger plasmid AMYP2 (71,487 bp), also named pEA72. The small size of the _E. amylovora_ genome (3.8 Mb) in comparison with most free-living enterobacteria, including plant pathogens, with genomes of 4.5-5.5 Mb, and the preponderance of pseudogenes, genome reduction can have occurred via mutational inactivation and subsequent deletion and, as a consequence, has led to the loss of most of the genes involved in anaerobic respiration and fermentation found in typical, related enterobacteria, with the consecuent reduction of the capacity to live in anaerobic environments [42]. The genome sequence of _E. amylovora_ has revealed clear signs of pathoadaptation to the rosaceous plant environment. For example, T3 SS-related proteins are more similar to proteins of other plant pathogens than to proteins of closely related enterobacteria [42]. Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of _E. amylovora_ has allowed to describe the pan-genome of this species. The pan-genome contains 5751 coding sequences and is a highly conserved relative to other phytopathogenic bacteria, comprising on average 89% conserved core genes. While the chromosomes of Spiraeoideae-infecting strains are highly homogeneous, greater genetic diversity was observed between Spiraeoideae- and _Rubus_-infecting strains (and among individual _Rubus_-infecting strains) [20]. Using molecular approaches based on the study of repetitive elements, such as Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) [59] or sequencing of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) [60], this diversity has also been especially observed among strains isolated from _Rubus_ plants and, to a lesser extent, in Spiraeoideae-infecting strains [48]. In comparison with other plant pathogens, however, _E. amylovora_ has relatively low genetic diversity, with a limited genetic recombination, this being associated with its exposure to limited selection pressures due to pome fruit breeding strategically favoring only high-valued varieties, which are often highly susceptible to fire blight [20, 61, 62]. On the basis of the current available data, it has been hypothesized that the critical event for adaptation to _Rubus_ spp. took place after species separation of _E. amylovora_ and _E. pyrifoliaie_, as the Spiraeoideae infecting isolates of _E. amylovora_ and _E. pyrifoliaie_ (including Japanese strains), as well as _E. tasmaniensis_ and _E. piriflorinigrans_, all sharing the Spiraeoideae-type LPS biosynthetic cluster [48]. Interestingly, genome sequencing of three Mexican _E. amylovora_ strains have revealed an _rpsL_chromosal mutation conferring high-level of streptomycin resistance [63]. This chromosomal mutation is the predominant _E. amylovora_ mechanism, typically appearing after years of intensive application with long persistence in populations [10, 63], explaining the observed inefficacy of streptomycin in Mexico [63, 64] and underscoring the need of revision of pesticide use strategies to avoid similar resistance evolution against other antimicrobial drugs as oxytetracycline or gentamicin [63]. The expression of genes related to starvation, oxidative stress, motility, pathogenicity, and virulence have been detected during the entire experimental period with different regulation patterns observed during the first 24 h. Further, starved cells remained as virulent as nonstressed cells. Overall, these results provide new knowledge on the biology of _E. amylovora_ under conditions prevailing in nature, which could contribute to a better understanding of the life cycle of this pathogen [46]. No major differences among 12 strains of _E. amylovora_ were reported in the amylovoran biosynthesis cluster (\(>\)98% amino acid indentity across the whole region) [20].