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The plant pathogen  Erwinia amylovora  can be divided into two host-specific groupings; strains infecting a broad range of hosts within the  Rosaceae  subfamily Spiraeoideae (e.g.,  Malus ,  Pyrus ,  Crataegus ,  Sorbus ) and strains infecting  Rubus  (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of  E. amylovora  was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and  Rubus -infecting strains (and among individual  Rubus -infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the  Rubus -infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of  E. amylovora  than it was to the other  Rubus -infecting strains. Analysis of the accessory genomes of Spiraeoideae- and  Rubus -infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1 Ea  and a putative secondary metabolite pathway only present in  Rubus -infecting strains.

Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core