Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance

• Published in: Genomics (San Diego, Calif.) Calif.), 2020-09, Vol.112 (5), p.3762-3772
• Main Authors: Parcey, Michael, Gayder, Steven, Morley-Senkler, Vivian, Bakkeren, Guus, Úrbez-Torres, José Ramón, Ali, Shawkat, Castle, Alan J., Svircev, Antonet M.
• Format: Article
• Language: English
• Subjects: Comparative genomics; Erwinia amylovora; Fire blight; Phytopathogen; Streptomycin resistance
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.04.001

Erwinia amylovora is a destructive pathogen of Rosaceous plants and an economic concern worldwide. Herein, we report 93 new E. amylovora genomes from North America, Europe, the Mediterranean, and New Zealand. This new genomic information demonstrates the existence of three primary clades of Amygdaloideae (apple and pear) infecting E. amylovora and suggests all three independently originate from North America. The comprehensive sequencing also identified and confirmed the presence of 7 novel plasmids ranging in size from 2.9 to 34.7 kbp. While the function of the novel plasmids is unknown, the plasmids pEAR27, pEAR28, and pEAR35 encoded for type IV secretion systems. The strA-strB gene pair and the K43R point mutation at codon 43 of the rpsL gene have been previously documented to confer streptomycin resistance. Of the sequenced isolates, rpsL-based streptomycin resistance was more common and was found with the highest frequency in the Western North American clade. •There are three primarily Amygdaloideae-infecting clades of E. amylovora.•rpsL-based streptomycin resistance was found most commonly in the Western North American clade of E. amylovora.•Seven novel plasmids were identified and confirmed ranging in size from 2.9 to 34.7 kbp.•Plasmid pEA29 can be used to determine the phylogenetic arrangement of E. amylovora.