ARTICLE Comparative genomics of Japanese Erwinia pyrifoliae strain Ejp617 with closely related erwinias Shree P. Thapa, Duck H. Park, Won S. Kim, Beom S. Choi, Jong S. Lim, Ik Y. Choi, Jang H. Hur, and Chun K. Lim Abstract: Japanese Erwinia pyrifoliae strains cause bacterial shoot blight of pear (BSBP) in Japan. The genetics of Japanese Erwinia remains largely unknown relative to the abundant genomic information available for other Erwinia strains. We compared the genome of Japanese and Korean E. pyrifoliae strains along with those of E. amylovora and E. tasmaniensis. Comparisons with the Korean E. pyrifoliae strain revealed numerous gene insertions/deletions, rearrangements, and inver- sions in the central regions of the chromosomes. Approximately 80% (2843) of coding DNA sequences (CDSs) are shared by these two genomes which represent about three-quarters of the genome, and there are about 20% unique CDSs. Compar- ative analysis with closely related erwinias showed that 1942 (more than 50%) core open reading frames (ORF) are shared by all these strains. In addition to two type III secretion systems (hrp/dsp and inv/spa), the genome of Ejp617 encodes numerous virulence factors, including a type VI secretion system, an exopolysaccharide synthesis cluster, and another protein secretion system present in plant pathogenic Erwinia strains. The availability of whole genome sequence should provide a resource to further improve the understanding of pathogenesis in Japanese E. pyrifoliae Ejp617 and to facilitate evolutionary studies among the species of the genus Erwinia. Key words: bacterial shoot blight, Japanese Erwinia pyrifoliae, whole genome, pathogenicity genes. Résumé : Les souches japonaises de l'Erwinia pyrifoliae causent le feu bactérien au Japon. La génétique des Erwinia japonais demeure largement inconnue en comparaison avec l'information génomique abondante au sujet d'autres souches de l'Erwinia. Les auteurs ont comparé les génomes de souches japonaises et coréennes de l'E. pyrifoliae avec ceux de l'E. amylovora et de l'E. tasmaniensis. Les comparaisons avec les souches coréennes de l'E. pyrifoliae ont révélé de nombreux réarrangements, insertions/ délétions et inversions au sein des régions centrales des chromosomes. Environ 80 % (2843) des régions codantes étaient communes aux deux génomes ce qui représente environ trois quarts du génome, et il y avait environ 20 % de séquences codantes uniques. Des analyses comparées avec des Erwinia apparentés ont montré que 1942 (plus de 50 %) des cadres de lecture communs étaient partagés par toutes ces souches. En plus de deux systèmes de sécrétion de type II (hrp/dsp et inv/spa), le génome de la souche Ejp617 code pour de nombreux facteurs de virulence, incluant un système de sécrétion de type VI, un amas de gènes pour la synthèse d'exopolysaccharides et un autre système de sécrétion protéique présent chez des souches phytopathogènes de l'Erwinia. La disponibilité de la séquence du génome entier procure une ressource de plus pour approfondir la connaissance de la pathogenèse chez la souche japonaise Ejp617 de l'E. pyrifoliae ainsi que pour faciliter les études évolutives parmi les espèces du genre Erwinia. [Traduit par la Rédaction] Mots-clés : feu bactérien, Erwinia pyrifoliae japonais, génome complet, gènes de pathogénicité. Introduction Japanese Erwinia strains causing bacterial shoot blight of pear (BSBP) were first isolated from Nashi pears in Hokkaido, Japan (Beer et al. 1996). The disease symptoms were almost indistin- guishable to those of Erwinia amylovora, the causative agent of fire blight disease in pome fruits and variety of Rosaceae species (Beer et al. 1996). Because of the similarity in disease symptoms, the pathogens were provisionally described as E. amylovora (Beer et al. 1996). During the early 1970s it evoked issues in trading of Japa- nese pear to blight free countries. Recent characterization of a new pathogen, Erwinia pyrifoliae on Asian pear in Korea, stimu- lated the need to reinvestigate the Japanese strains (Kim et al. 1999; Shrestha et al. 2003). Several biochemical and molecular studies suggested that the Japanese Erwinia strains were more similar to E. pyrifoliae than to E. amylovora (Kim et al. 2001; Maxon-Stein et al. 2003; Jock and Geider 2004; Matsuura et al. 2007; Waleron et al. 2008), resulting in designation of the Japa- nese strains as E. pyrifoliae on the basis of a polyphasic approach (Geider et al. 2009). Only a few Japanese strains are available so far, and thus limited information is known about these pathogens. Therefore, it neces- sitates complete genome analysis of these pathogens both to un- ravel the genetic basis behind the pathogenesis and fitness of these strains as well as to trace the gene ontology of these species. We have recently completed the analysis of whole genome se- quence of Japanese E. pyrifoliae strain Ejp617 (Park et al. 2011). As this was the first report on the genome sequence of a Japanese E. pyrifoliae, the central characteristic features of this microbe is still largely unknown. Here, we unlashed the whole genome se- quence of Japanese E. pyrifoliae Ejp617 and compared it with the Received 28 June 2012. Accepted 22 November 2012. Corresponding Editor: J. Bell. S.P. Thapa and J.H. Hur. Department of Biological Environment, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Korea. D.H. Park and C.K. Lim. Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Korea. W.S. Kim. Norgen Biotek Corporation, Thorold, ON L2V 4Y6, Canada. B.S. Choi, J.S. Lim, and I.Y. Choi. NIECM, College of Agriculture and Life Sciences, Seoul National University, Gwanangno 599, Gwanak-gu, Seoul 151-921, Republic of Korea. Corresponding authors: J.H. Hur (e-mail: jhhur@kangwon.ac.kr) and C.K. Lim (e-mail: chunkeun@kangwon.ac.kr). 83 Genome 56: 83–90 (2013) dx.doi.org/10.1139/gen-2012-0094 Published at www.nrcresearchpress.com/gen on 14 December 2012. Genome Downloaded from www.nrcresearchpress.com by Calif Dig Lib - Davis on 04/02/14 For personal use only.