Molecular Population Genetics of Elicitor-Induced Resistance Genes in European Aspen (Populus tremula L., Salicaceae)
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{"title"=>"Molecular population genetics of elicitor-induced resistance genes in european aspen (Populus tremula L., Salicaceae)", "type"=>"journal", "authors"=>[{"first_name"=>"Carolina", "last_name"=>"Bernhardsson", "scopus_author_id"=>"35073526400"}, {"first_name"=>"Pär K.", "last_name"=>"Ingvarsson", "scopus_author_id"=>"7003949499"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"362577543", "doi"=>"10.1371/journal.pone.0024867", "scopus"=>"2-s2.0-80052903048", "sgr"=>"80052903048", "issn"=>"19326203", "pmid"=>"21949772"}, "id"=>"8ee34e4b-9ee1-3797-93a9-172df03e274f", "abstract"=>"Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated K(A)/K(S) ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution.", "link"=>"http://www.mendeley.com/research/molecular-population-genetics-elicitorinduced-resistance-genes-european-aspen-populus-tremula-l-sali", "reader_count"=>51, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>42, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Psychology"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>42}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>3, "Norway"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/370407"], "description"=>"<div><p>Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, <em>Populus tremula</em>, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene <em>PPO1</em> has a 600 bp region with a highly elevated K<sub>A</sub>/K<sub>S</sub> ratio and reduced synonymous diversity. <em>PPO1</em> also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that <em>PPO1</em> has been subjected to recurrent selective sweeps. The gene <em>PPO2</em> shows a marked excess of high frequency, derived variants and shows many of the same trends as <em>PPO1</em> does, even though the pattern is less pronounced, suggesting that <em>PPO2</em> might have been the target of a recent selective sweep. Our results supports data from both <em>Populus</em> and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution.</p> </div>", "links"=>[], "tags"=>["molecular", "genetics", "elicitor-induced", "genes", "european", "aspen"], "article_id"=>133185, "categories"=>["Cell Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Population_Genetics_of_Elicitor_Induced_Resistance_Genes_in_European_Aspen_Populus_tremula_L_Salicaceae_/133185", "title"=>"Molecular Population Genetics of Elicitor-Induced Resistance Genes in European Aspen (<em>Populus tremula</em> L., Salicaceae)", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-19 00:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/733666"], "description"=>"<p>Number of fixed and polymorphic mutations at synonymous and replacement sites in the coding regions of <i>Populus tremula</i> inducible defense genes.</p>", "links"=>[], "tags"=>["polymorphic", "mutations", "synonymous", "sites", "coding", "regions", "inducible"], "article_id"=>404018, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_fixed_and_polymorphic_mutations_at_synonymous_and_replacement_sites_in_the_coding_regions_of_Populus_tremula_inducible_defense_genes_/404018", "title"=>"Number of fixed and polymorphic mutations at synonymous and replacement sites in the coding regions of <i>Populus tremula</i> inducible defense genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-19 01:06:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/733359"], "description"=>"<p>Values plotted are the midpoints of windows 75 bp wide at 8 bp increments. The corresponding gene structures are shown at the bottom of the plots: exons are indicated by boxes and non-coding regions (introns and UTRs) by lines.</p>", "links"=>[], "tags"=>["intraspecific", "synonymous", "sites"], "article_id"=>403717, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sliding_window_of_intraspecific_diversity_at_synonymous_sites_syn_/403717", "title"=>"Sliding window of intraspecific diversity at synonymous sites (π<sub>syn</sub>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:01:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/733628"], "description"=>"<p>N, number of sampled haplotypes; Sites, length of gene regions surveyed; S, number of segregating sites; π<sub>tot</sub>, π<sub>syn</sub>, π<sub>rep</sub>, average pairwise diversity per site for total, synonymous, and replacement sites, respectively; K<sub>syn</sub>, K<sub>rep</sub>, divergence calculated from <i>P. trichocarpa</i> for synonymous, and replacement sites, respectively; H<sub>norm</sub>, Fay and Wu's normalized H; D, Tajima's D. Data for genome-wide average are from Ingvarsson <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024867#pone.0024867-Ingvarsson2\" target=\"_blank\">[34]</a>.</p><p>*p = 0.05,</p><p>**p = 0.01.</p>", "links"=>[], "tags"=>["inducible", "genes", "genome-wide", "calculated", "76"], "article_id"=>403984, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_eight_inducible_defense_genes_and_a_genome_wide_average_calculated_over_76_reference_genes_/403984", "title"=>"Summary statistics of eight inducible defense genes and a genome-wide average calculated over 76 reference genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-19 01:06:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/733302"], "description"=>"<p>Data sets were obtained from Ralph et al. (2006) (denoted by PT), Sterky et al (2004) (denoted by PopulusDB) or from unpublished data from the Arborea project (<a href=\"http://www.arborea.ulaval.ca/\" target=\"_blank\">http://www.arborea.ulaval.ca/</a>, denoted Arborea). Data sets obtained from normalized libraries are denoted by *. Wound induction gives the relative expression in data sets obtained from wounded or infected tissues compared to normal tissues.</p>", "links"=>[], "tags"=>["analyses", "defense-associated", "genes"], "article_id"=>403655, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_of_digital_northern_analyses_of_expression_data_for_eight_defense_associated_genes_in_Populus_/403655", "title"=>"Heat map of digital northern analyses of expression data for eight defense-associated genes in <i>Populus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:00:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/733510"], "description"=>"<p>Values plotted are the midpoints of windows 250 bp wide at 25 bp increments. Dotted line indicates the 95 percentile of the K<sub>A</sub>/K<sub>S</sub> ratio for the 76 control loci (see text for further details) which is equal to 1.14.The corresponding gene structures are shown at the bottom of the plots: exons are indicated by boxes and non-coding regions (introns and UTRs) by lines.</p>", "links"=>[], "tags"=>["nonsynonymous-to-synonymous", "divergence"], "article_id"=>403867, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Carolina Bernhardsson", "Pär K. Ingvarsson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024867.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sliding_window_of_nonsynonymous_to_synonymous_ratio_of_diversity_red_line_and_divergence_black_line_/403867", "title"=>"Sliding window of nonsynonymous-to-synonymous ratio of diversity (red line) and divergence (black line).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:04:27"}

PMC Usage Stats | Further Information

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Relative Metric

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