Genome Sequence of an Erwinia amylovora Strain with Pathogenicity Restricted to Rubus Plants

Abstract

Here, we present the genome of a strain of Erwinia amylovora, the fire blight pathogen, with pathogenicity restricted to Rubus spp. Comparative genomics of ATCC BAA-2158 with E. amylovora strains from non-Rubus hosts identified significant genetic differences but support the inclusion of this strain within the species E. amylovora.

Erwinia amylovora is a Gram-negative enterobacterial phytopathogen that was first reported from the Northeastern United States in the late 1790s (2). Most strains of E. amylovora have broad-spectrum pathogenicity to plants of the Spiraeoideae subfamily (revised Maloideae), particularly commercial apple and pear and ornamental and amenity species that include members of the genera Sorbus, Crataegus, and Cotoneaster (2). However, a less common, genetically distinct group of E. amylovora strains with a host range restricted to Rubus species has also been described from North America (9, 13). Here, we report the first genome sequence of a Rubus-pathogenic E. amylovora strain, ATCC BAA-2158 (syn. Ea246, Bb-1, IL-5), isolated from thornless blackberry in Illinois (9).

This sequence augments genomic data from recently sequenced Spiraeoideae-pathogenic strains of E. amylovora ATCC 49946 (10) and CFBP 1430 (12) and genomes of the closely related Erwinia species E. pyrifoliae DSM 12163^T (pathogen of Asian pear) (11), E. tasmaniensis Et1/99 (epiphyte of uncertain pathogenicity) (5), and the nonpathogenic E. billingiae Eb661 (4). Our objective was to facilitate comparative studies that may elucidate the host-range determinants and evolutionary origins of this important phytopathogenic bacterial species.

Whole-genome pyrosequencing (454 Life Sciences) from two independent runs (3/8 of a 454 Titanium run and one 454 GS Junior run) yielded 344,879 high-quality filtered reads with an average read length of 375 bp and 31-times genome coverage. A consensus assembly of 32 contigs was obtained by assembly with Newbler (454 Life Sciences), and in silico gap closure performed with Lasergene (DNAStar, Madison, WI). Assembly was confirmed by realigning reads against the consensus using NGen 2.0 (DNAStar).

The E. amylovora ATCC BAA-2158 genome contains a chromosome (3.81 Mb in 29 contigs with 53.6% G+C content) and three circular plasmids, pEA29 (28,138 bp with 50% G+C), pEAR5.2 (5,251 bp with 52.2% G+C), and pEAR4.3 (4,369 bp with 51.5% G+C). A total of 3,869 coding sequences (CDS) and putative functions of the encoding genes were automatically assigned to the genome using GenDB (8) with manual optimization (11, 12). Plasmid pEA29 shares 99% sequence identity (100% coverage) with previously described pEA29 plasmids in genotypically diverse strains of E. amylovora (6, 10, 12). Plasmids pEAR5.2 (6 CDS) and pEAR4.3 (4 CDS) are unique to strain ATCC BAA-2158 and share 88% and 89% sequence identity (57% and 53% coverage) with pEP5 of E. pyrifoliae DSM 12163^T (11).

Genomic sequence comparison using EDGAR (1) revealed approximately 373 singletons from ATCC BAA-2158 that were absent or highly divergent in the genomes of Spiraeoideae-infecting strains CFPB 1430 and ATCC 49946 of E. amylovora (10, 12). However, genomic sequence comparison of ATCC BAA-2158 with these strains of E. amylovora and the closely related species E. pyrifoliae DSM 12163^T (11), E. tasmaniensis Et1/99 (5), and E. billingiae Eb661 (4) corroborates other analyses (e.g., DNA-DNA hybridization and sequencing of housekeeping genes) that retain ATCC BAA-2158 within the species E. amylovora (3, 7).

Nucleotide sequence accession numbers.

The 29 contigs of the draft chromosome of E. amylovora strain ATCC BAA-2158 were deposited at EMBL under accession numbers FR719181 to FR719209, and the plasmids under accession numbers FR719212 (pEA29), FR719210 (pEAR4.3), and FR719211 (pEAR5.2).