A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum

Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic...

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Published inBMC ecology and evolution Vol. 19; no. 1; pp. 123 - 16
Main Authors Castillo, José A., Agathos, Spiros N.
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 17.06.2019
BioMed Central
BMC
Subjects
Alleles
Bacteria
Balancing
Balancing selection
Biodiversity
Bioinformatics
Biological Evolution
Blood diseases
Burkholderia
Chromosomes
Defense industry
Defense mechanisms
Demographics
Deoxyribonucleic acid
Disease
Dismantling
DNA
Evolutionary genetics
Extreme values
Fitness
Fu & Li’s D
Gene pool
Genes
Genetic aspects
Genetic diversity
Genetics
Genome, Bacterial
Genome-wide association studies
Genomes
Genomics
Host plants
Host range
Host Specificity
Immune response
Metabolism
Mutation
Pathogenic microorganisms
Pathogens
Phylogenetics
Plant bacterial diseases
Plant Diseases - microbiology
Plant immunity
Plant resistance
Plants
Polymorphism
Population
Population genetics
Population statistics
Populations
Prospective Studies
Ralstonia solanacearum
Ralstonia solanacearum - cytology
Ralstonia solanacearum - genetics
Ralstonia solanacearum - pathogenicity
Reproductive fitness
Species
Statistical analysis
Tajima’s D
Virulence
Virulence (Microbiology)
Virulence related genes
Watterson’s theta
Wilt
Ralstonia solanacearum
Pathogenesis
Balancing selection
Virulence related genes
Fu & Li’s D
Watterson’s theta
Tajima’s D
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Abstract Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'. Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, θ and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
AbstractList Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'.BACKGROUNDPlant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'.Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, θw and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process.RESULTSUsing a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, θw and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process.We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.CONCLUSIONSWe identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'. Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, [theta].sub.w and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Results Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. Conclusions We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
Abstract Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Results Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. Conclusions We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'. Results Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, [theta].sub.w and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. Conclusions We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses. Keywords: Balancing selection, Ralstonia solanacearum, Tajima's D, Watterson's theta, Fu & Li's D*, Virulence related genes, Pathogenesis
Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen's gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called 'bacterial wilt'. Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima's D, θ and Fu & Li's D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
ArticleNumber 123
Audience Academic
Author Agathos, Spiros N.
Castillo, José A.
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Issue 1
Keywords Ralstonia solanacearum
Pathogenesis
Balancing selection
Virulence related genes
Fu & Li’s D
Watterson’s theta
Tajima’s D
Language English
License Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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Snippet Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to...
Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or...
Abstract Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this...
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SubjectTerms Alleles
Bacteria
Balancing
Balancing selection
Biodiversity
Bioinformatics
Biological Evolution
Blood diseases
Burkholderia
Chromosomes
Defense industry
Defense mechanisms
Demographics
Deoxyribonucleic acid
Disease
Dismantling
DNA
Evolutionary genetics
Extreme values
Fitness
Fu & Li’s D
Gene pool
Genes
Genetic aspects
Genetic diversity
Genetics
Genome, Bacterial
Genome-wide association studies
Genomes
Genomics
Host plants
Host range
Host Specificity
Immune response
Metabolism
Mutation
Pathogenic microorganisms
Pathogens
Phylogenetics
Plant bacterial diseases
Plant Diseases - microbiology
Plant immunity
Plant resistance
Plants
Polymorphism
Population
Population genetics
Population statistics
Populations
Prospective Studies
Ralstonia solanacearum
Ralstonia solanacearum - cytology
Ralstonia solanacearum - genetics
Ralstonia solanacearum - pathogenicity
Reproductive fitness
Species
Statistical analysis
Tajima’s D
Virulence
Virulence (Microbiology)
Virulence related genes
Watterson’s theta
Wilt
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Title A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum
URI https://www.ncbi.nlm.nih.gov/pubmed/31208326
https://www.proquest.com/docview/2242611024
https://www.proquest.com/docview/2546690738
https://www.proquest.com/docview/2242819258
https://pubmed.ncbi.nlm.nih.gov/PMC6580516
https://doaj.org/article/e509ecbc3bd24ac7af2393383abf86e2
Volume 19
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