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Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora

The fire blight pathogen, Erwinia amylovora (EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains. However, the genomic aspects of population bottlenecks and selecti...

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Autores principales: Singh, Jugpreet, Khan, Awais
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768868/
https://www.ncbi.nlm.nih.gov/pubmed/31570749
http://dx.doi.org/10.1038/s41598-019-50589-z
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author Singh, Jugpreet
Khan, Awais
author_facet Singh, Jugpreet
Khan, Awais
author_sort Singh, Jugpreet
collection PubMed
description The fire blight pathogen, Erwinia amylovora (EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains. However, the genomic aspects of population bottlenecks and selection pressure from geographical isolation, host range, and management practices are yet unexplored. We conducted a comprehensive analysis of whole genome sequences of 41 strains to study genetic diversity, population structure, and the nature of selection affecting sub-population differentiation in EA. We detected 72,741 SNPs and 2,500 Indels, representing about six-fold more diversity than previous reports. Moreover, nonsynonymous substitutions were identified across the effector regions, suggesting a role in defining virulence of specific strains. EA plasmids had more diversity than the chromosome sequence. Population structure analysis identified three distinct sub-groups in EA strains, with North American strains displaying highest genetic diversity. A five kilobase genomic window scan showed differences in genomic diversity and selection pressure between these three sub-groups. This analysis also highlighted the role of purifying and balancing selection in shaping EA genome structure. Our analysis provides novel insights into the genomic diversity and selection forces accompanying EA population differentiation.
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spelling pubmed-67688682019-10-04 Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora Singh, Jugpreet Khan, Awais Sci Rep Article The fire blight pathogen, Erwinia amylovora (EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains. However, the genomic aspects of population bottlenecks and selection pressure from geographical isolation, host range, and management practices are yet unexplored. We conducted a comprehensive analysis of whole genome sequences of 41 strains to study genetic diversity, population structure, and the nature of selection affecting sub-population differentiation in EA. We detected 72,741 SNPs and 2,500 Indels, representing about six-fold more diversity than previous reports. Moreover, nonsynonymous substitutions were identified across the effector regions, suggesting a role in defining virulence of specific strains. EA plasmids had more diversity than the chromosome sequence. Population structure analysis identified three distinct sub-groups in EA strains, with North American strains displaying highest genetic diversity. A five kilobase genomic window scan showed differences in genomic diversity and selection pressure between these three sub-groups. This analysis also highlighted the role of purifying and balancing selection in shaping EA genome structure. Our analysis provides novel insights into the genomic diversity and selection forces accompanying EA population differentiation. Nature Publishing Group UK 2019-09-30 /pmc/articles/PMC6768868/ /pubmed/31570749 http://dx.doi.org/10.1038/s41598-019-50589-z Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Singh, Jugpreet
Khan, Awais
Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title_full Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title_fullStr Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title_full_unstemmed Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title_short Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
title_sort distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, erwinia amylovora
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768868/
https://www.ncbi.nlm.nih.gov/pubmed/31570749
http://dx.doi.org/10.1038/s41598-019-50589-z
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