title: Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.
abstract: 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.
authors: Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia.
authors: Rachel A
authors: RA
authors: Mann
authors: Theo H M
authors: TH
authors: Smits
authors: Andreas
authors: A
authors: Bühlmann
authors: Jochen
authors: J
authors: Blom
authors: Alexander
authors: A
authors: Goesmann
authors: Jürg E
authors: JE
authors: Frey
authors: Kim M
authors: KM
authors: Plummer
authors: Steven V
authors: SV
authors: Beer
authors: Joanne
authors: J
authors: Luck
authors: Brion
authors: B
authors: Duffy
authors: Brendan
authors: B
authors: Rodoni
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D044084:Erwinia amylovora / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial