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Patterns of genomic variations in the plant pathogen Dickeya solani

The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of sev...

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Main Authors: Khayi, Slimane, Chan, Kok-Gan, Faure, Denis
Format: Article
Published: MDPI 2022
Subjects:
GE Environmental Sciences
S Agriculture (General)
Online Access:http://eprints.um.edu.my/46203/
https://doi.org/10.3390/microorganisms10112254
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spelling my.um.eprints.462032024-10-22T06:13:03Z http://eprints.um.edu.my/46203/ Patterns of genomic variations in the plant pathogen Dickeya solani Khayi, Slimane Chan, Kok-Gan Faure, Denis GE Environmental Sciences S Agriculture (General) The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani. MDPI 2022-11 Article PeerReviewed Khayi, Slimane and Chan, Kok-Gan and Faure, Denis (2022) Patterns of genomic variations in the plant pathogen Dickeya solani. Microorganisms, 10 (11). ISSN 2076-2607, DOI https://doi.org/10.3390/microorganisms10112254 <https://doi.org/10.3390/microorganisms10112254>. https://doi.org/10.3390/microorganisms10112254 10.3390/microorganisms10112254
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic GE Environmental Sciences
S Agriculture (General)
spellingShingle GE Environmental Sciences
S Agriculture (General)
Khayi, Slimane
Chan, Kok-Gan
Faure, Denis
Patterns of genomic variations in the plant pathogen Dickeya solani
description The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani.
format Article
author Khayi, Slimane
Chan, Kok-Gan
Faure, Denis
author_facet Khayi, Slimane
Chan, Kok-Gan
Faure, Denis
author_sort Khayi, Slimane
title Patterns of genomic variations in the plant pathogen Dickeya solani
title_short Patterns of genomic variations in the plant pathogen Dickeya solani
title_full Patterns of genomic variations in the plant pathogen Dickeya solani
title_fullStr Patterns of genomic variations in the plant pathogen Dickeya solani
title_full_unstemmed Patterns of genomic variations in the plant pathogen Dickeya solani
title_sort patterns of genomic variations in the plant pathogen dickeya solani
publisher MDPI
publishDate 2022
url http://eprints.um.edu.my/46203/
https://doi.org/10.3390/microorganisms10112254
_version_ 1814047580678520832
score 13.211869

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