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

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

doi:10.21256/zhaw-1469

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-1469

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core
Authors:	Mann, Rachel A. Smits, Theo H.M. Bühlmann, Andreas Blom, Jochen Goesmann, Alexander Frey, Jürg E. Plummer, Kim M. Beer, Steven V. Luck, Joanne Duffy, Brion Rodoni, Brendan
DOI:	10.21256/zhaw-1469 10.1371/journal.pone.0055644
Published in:	PLOS ONE
Volume(Issue):	8
Issue:	2
Issue Date:	7-Feb-2013
Publisher / Ed. Institution:	Public Library of Science
Publisher / Ed. Institution:	San Francisco
ISSN:	1932-6203
Language:	English
Subject (DDC):	570: Biology
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 HopX1Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains.
URI:	https://digitalcollection.zhaw.ch/handle/11475/1591
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Natural Resource Sciences (IUNR)
Published as part of the ZHAW project:	Genomik und Transkriptomik von Erwinia und Pantoea
Appears in collections:	Publikationen Life Sciences und Facility Management

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Mann, R. A., Smits, T. H. M., Bühlmann, A., Blom, J., Goesmann, A., Frey, J. E., Plummer, K. M., Beer, S. V., Luck, J., Duffy, B., & Rodoni, B. (2013). Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. Plos One, 8(2). https://doi.org/10.21256/zhaw-1469

Mann, R.A. et al. (2013) ‘Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core’, PLOS ONE, 8(2). Available at: https://doi.org/10.21256/zhaw-1469.

R. A. Mann et al., “Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core,” PLOS ONE, vol. 8, no. 2, Feb. 2013, doi: 10.21256/zhaw-1469.

MANN, Rachel A., Theo H.M. SMITS, Andreas BÜHLMANN, Jochen BLOM, Alexander GOESMANN, Jürg E. FREY, Kim M. PLUMMER, Steven V. BEER, Joanne LUCK, Brion DUFFY und Brendan RODONI, 2013. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PLOS ONE. 7 Februar 2013. Bd. 8, Nr. 2. DOI 10.21256/zhaw-1469

Mann, Rachel A., Theo H.M. Smits, Andreas Bühlmann, Jochen Blom, Alexander Goesmann, Jürg E. Frey, Kim M. Plummer, et al. 2013. “Comparative Genomics of 12 Strains of Erwinia Amylovora Identifies a Pan-Genome with a Large Conserved Core.” Plos One 8 (2). https://doi.org/10.21256/zhaw-1469.

Mann, Rachel A., et al. “Comparative Genomics of 12 Strains of Erwinia Amylovora Identifies a Pan-Genome with a Large Conserved Core.” Plos One, vol. 8, no. 2, Feb. 2013, https://doi.org/10.21256/zhaw-1469.