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Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core
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 o...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567147/ https://www.ncbi.nlm.nih.gov/pubmed/23409014 http://dx.doi.org/10.1371/journal.pone.0055644 |
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author | 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 |
author_facet | 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 |
author_sort | Mann, Rachel A. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3567147 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35671472013-02-13 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 PLoS One Research Article 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. Public Library of Science 2013-02-07 /pmc/articles/PMC3567147/ /pubmed/23409014 http://dx.doi.org/10.1371/journal.pone.0055644 Text en © 2013 Mann et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article 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 Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title | Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title_full | Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title_fullStr | Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title_full_unstemmed | Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title_short | Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core |
title_sort | comparative genomics of 12 strains of erwinia amylovora identifies a pan-genome with a large conserved core |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567147/ https://www.ncbi.nlm.nih.gov/pubmed/23409014 http://dx.doi.org/10.1371/journal.pone.0055644 |
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