Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core

Rachel A Mann; Theo H M Smits; Andreas Bühlmann; Jochen Blom; Alexander Goesmann; Jürg E Frey; Kim M Plummer; Steven V Beer; Joanne Luck; Brion Duffy; Brendan Rodoni

doi:10.1371/journal.pone.0055644

Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core

PLoS One. 2013;8(2):e55644. doi: 10.1371/journal.pone.0055644. Epub 2013 Feb 7.

Authors

Rachel A Mann¹, Theo H M Smits, Andreas Bühlmann, Jochen Blom, Alexander Goesmann, Jürg E Frey, Kim M Plummer, Steven V Beer, Joanne Luck, Brion Duffy, Brendan Rodoni

Affiliation

¹ Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia.

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.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

DNA, Bacterial / genetics
Erwinia amylovora / classification
Erwinia amylovora / genetics*
Genome, Bacterial*
Phylogeny
Species Specificity

Substances

DNA, Bacterial

Grants and funding

The authors would like to acknowledge the support of the Australian Government’s Cooperative Research Centre’s program, Horticulture Australia Limited, a Special Grant provided by the United States Department of Agriculture CSREES for research on fire blight in New York and the Swiss Federal Office of Agriculture (BLW Nr. 08.02). This research was conducted in part within the European Science Foundation funded research network COST Action 864. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.