Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease
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{"title"=>"Transcriptome profiling of citrus fruit response to huanglongbing disease", "type"=>"journal", "authors"=>[{"first_name"=>"Federico", "last_name"=>"Martinelli", "scopus_author_id"=>"56308398900"}, {"first_name"=>"Sandra L.", "last_name"=>"Uratsu", "scopus_author_id"=>"6602179715"}, {"first_name"=>"Ute", "last_name"=>"Albrecht", "scopus_author_id"=>"56261720400"}, {"first_name"=>"Russell L.", "last_name"=>"Reagan", "scopus_author_id"=>"35088820800"}, {"first_name"=>"My L.", "last_name"=>"Phu", "scopus_author_id"=>"37047506700"}, {"first_name"=>"Monica", "last_name"=>"Britton", "scopus_author_id"=>"53866196600"}, {"first_name"=>"Vincent", "last_name"=>"Buffalo", "scopus_author_id"=>"54796402100"}, {"first_name"=>"Joseph", "last_name"=>"Fass", "scopus_author_id"=>"7007057179"}, {"first_name"=>"Elizabeth", "last_name"=>"Leicht", "scopus_author_id"=>"12647293200"}, {"first_name"=>"Weixiang", "last_name"=>"Zhao", "scopus_author_id"=>"7403943470"}, {"first_name"=>"Dawei", "last_name"=>"Lin", "scopus_author_id"=>"8905703100"}, {"first_name"=>"Raissa", "last_name"=>"D'Souza", "scopus_author_id"=>"15724297700"}, {"first_name"=>"Cristina E.", "last_name"=>"Davis", "scopus_author_id"=>"8871982300"}, {"first_name"=>"Kim D.", "last_name"=>"Bowman", "scopus_author_id"=>"7103098715"}, {"first_name"=>"Abhaya M.", "last_name"=>"Dandekar", "scopus_author_id"=>"35564951100"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"364923212", "sgr"=>"84861663267", "issn"=>"19326203", "pmid"=>"22675433", "scopus"=>"2-s2.0-84861663267", "doi"=>"10.1371/journal.pone.0038039", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"4648fd9e-c54f-3f2b-9277-0aebbec20b19", "abstract"=>"Huanglongbing (HLB) or \"citrus greening\" is the most destructive citrus disease worldwide. 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HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. 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  • {"files"=>["https://ndownloader.figshare.com/files/326785", "https://ndownloader.figshare.com/files/326811", "https://ndownloader.figshare.com/files/326832", "https://ndownloader.figshare.com/files/326870", "https://ndownloader.figshare.com/files/326886", "https://ndownloader.figshare.com/files/326913", "https://ndownloader.figshare.com/files/326936", "https://ndownloader.figshare.com/files/326952", "https://ndownloader.figshare.com/files/326976", "https://ndownloader.figshare.com/files/327004", "https://ndownloader.figshare.com/files/327061"], "description"=>"<div><p>Huanglongbing (HLB) or “citrus greening” is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with <em>Candidatus</em> Liberibacter <em>asiaticus</em> (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.</p> </div>", "links"=>[], "tags"=>["transcriptome", "profiling", "citrus", "huanglongbing"], "article_id"=>124490, "categories"=>["Genetics", "Cell Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.s001", "https://dx.doi.org/10.1371/journal.pone.0038039.s002", "https://dx.doi.org/10.1371/journal.pone.0038039.s003", "https://dx.doi.org/10.1371/journal.pone.0038039.s004", "https://dx.doi.org/10.1371/journal.pone.0038039.s005", "https://dx.doi.org/10.1371/journal.pone.0038039.s006", "https://dx.doi.org/10.1371/journal.pone.0038039.s007", "https://dx.doi.org/10.1371/journal.pone.0038039.s008", "https://dx.doi.org/10.1371/journal.pone.0038039.s009", "https://dx.doi.org/10.1371/journal.pone.0038039.s010", "https://dx.doi.org/10.1371/journal.pone.0038039.s011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptome_Profiling_of_Citrus_Fruit_Response_to_Huanglongbing_Disease/124490", "title"=>"Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-31 01:14:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/630485"], "description"=>"<p>Over-represented GO terms in four pairwise comparisons: symptomatic (SY) vs. apparently healthy (AH), symptomatic vs. asymptomatic (AS), symptomatic vs. apparently healthy and asymptomatic, asymptomatic vs. symptomatic. The size of the colored sector of each pie chart corresponds to the proportion of that GO term in the test set compared to all the genes to which that GO term has been assigned, where 100% colored means all of the genes in the reference set are in the test set. Colors correspond to the number of genes in the GO category on a log scale, as indicated by the scale bar.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology"], "article_id"=>300961, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fisher_s_Exact_Test_analysis_/300961", "title"=>"Fisher's Exact Test analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:16:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/630628"], "description"=>"<p>Metabolism overview in MapMan depicting differential gene expression in symptomatic and apparently healthy fruits from the infected orchard. Log fold ratios are indicated as a gradient between red (up-regulated) and green (down-regulated).</p>", "links"=>[], "tags"=>["categorization", "differentially", "regulated", "genes", "symptomatic"], "article_id"=>301102, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_categorization_of_differentially_regulated_genes_in_symptomatic_fruits_/301102", "title"=>"Functional categorization of differentially regulated genes in symptomatic fruits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:18:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/630753"], "description"=>"<p>Symptomatic fruit was compared to asymptomatic fruit within the same tree (AS), different tree (AH) and both trees. A) Light reactions of photosynthesis. B) Glycolysis. “CB” block shows gene expression in cytosolic branch genes of small carbohydrate metabolism. C) Sucrose and starch metabolism D) Raffinose metabolism. Colored data points indicate up or down expression with log fold ratios >0.5 and <−0.5, respectively.</p>", "links"=>[], "tags"=>["views", "differentially", "regulated", "metabolism"], "article_id"=>301226, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MapMan_views_of_differentially_regulated_primary_metabolism_genes_/301226", "title"=>"MapMan views of differentially regulated primary metabolism genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:20:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/630846"], "description"=>"<p>Differential expression of (A) hormone-related transcripts and (B) transcription factors. Color scale indicates the comparisons between symptomatic asymptomatic and apparently healthy fruit, same as used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038039#pone-0038039-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["transcription"], "article_id"=>301324, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HLB_altered_expression_of_hormone_and_transcription_factors_/301324", "title"=>"HLB-altered expression of hormone and transcription factors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:22:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/630930"], "description"=>"<p>Log fold ratios are indicated by a gradient from red (up-regulated) to green (down-regulated). Comparison was made between symptomatic and apparently healthy fruits from the infected orchard. A) Jasmonate biosynthesis, B) Terpenoid and carotenoid biosynthesis, C) Salicylic acid pathway.</p>", "links"=>[], "tags"=>["symptomatic", "volatile"], "article_id"=>301408, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HLB_altered_expression_in_symptomatic_fruit_in_volatile_and_defense_response_pathways_/301408", "title"=>"HLB-altered expression in symptomatic fruit in volatile and defense response pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:23:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/631015"], "description"=>"<p>A) Differentially expressed genes involved in ubiquitin-dependent degradation, showing comparison between symptomatic and apparently healthy fruits. B) Pattern of expression of heat shock protein 82 (HSP82) in HLB-free location (CO), apparently healthy (AH), asymptomatic (AS), and symptomatic (SY) fruits. C) Protein-protein interaction network predicted in <i>Citrus</i> based on the <i>Arabidopsis</i> knowledgebase. Networks between proteins encoded by HLB-regulated genes were divided into four different clusters. Node legend indicates functional classes of transcripts.</p>", "links"=>[], "tags"=>["degradation"], "article_id"=>301491, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HLB_altered_expression_related_to_protein_degradation_and_misfolding_/301491", "title"=>"HLB-altered expression related to protein degradation and misfolding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:24:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/631116"], "description"=>"<p>Pattern of expression of genes belonging to different pathways in the four categories of fruits: symptomatic (SY), asymptomatic (AS), apparently healthy (AH) and healthy from HLB-free location (CO). Gene names correspond to those listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038039#pone-0038039-t002\" target=\"_blank\">Table 2</a>. Bar heights for expression of Invertase also shown at 20-fold magnification (lower-right inset).</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology"], "article_id"=>301593, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qRT_PCR_analysis_/301593", "title"=>"qRT-PCR analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:26:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/631213"], "description"=>"<p>Genes, pathways, and cell functions that were differentially expressed are indicated with a square (red for up-regulated, green for down-regulated). Significantly differentially regulated pathways in gene set enrichment analysis are indicated in yellow.</p>", "links"=>[], "tags"=>["metabolism", "pathways", "calas-infected"], "article_id"=>301690, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fruit_metabolism_and_regulatory_pathways_in_CaLas_infected_fruits_/301690", "title"=>"Fruit metabolism and regulatory pathways in CaLas-infected fruits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:28:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/631347"], "description"=>"<p>Differentially regulated genes and pathways involved in primary metabolism are indicated with a square (red for up-regulated, green for down-regulated).</p>", "links"=>[], "tags"=>["metabolism", "symptomatic"], "article_id"=>301825, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HLB_regulation_of_primary_metabolism_in_symptomatic_fruits_/301825", "title"=>"HLB-regulation of primary metabolism in symptomatic fruits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:30:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/631498"], "description"=>"<p>(A) Fruits of apparently healthy plants; (B) Asymtomatic fruits of infected plants; (C) Symtomatic fruits of infected plants.</p>", "links"=>[], "tags"=>["fruits"], "article_id"=>301971, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Stages_of_infection_in_the_Citrus_fruits_studied_/301971", "title"=>"Stages of infection in the <i>Citrus</i> fruits studied.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 00:32:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/631670"], "description"=>"<p>Analysis was performed on the list of genes differentially expressed at a significance level of p<0.1 comparing symptomatic to asymptomatic fruits within tree and between different trees “N.s.” means not significant.</p>", "links"=>[], "tags"=>["regulated", "pathways", "hlb", "symptomatic"], "article_id"=>302144, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_regulated_pathways_up_and_down_regulated_involved_in_HLB_response_in_the_symptomatic_fruit_as_determined_using_Pathexpress_/302144", "title"=>"Differentially regulated pathways (up- and down-regulated) involved in HLB response in the symptomatic fruit as determined using Pathexpress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-31 00:35:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/631738"], "description"=>"<p>Names of genes (or abbreviated gene names in parentheses) correspond to bar clusters in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038039#pone-0038039-g007\" target=\"_blank\">Figure 7</a>. Symptomatic (SY), asymptomatic (AS), apparently healthy (AH), healthy control (CO). P-values<0.05 are considered significant.</p>", "links"=>[], "tags"=>["genes", "quantitative", "p-values", "pairwise", "comparisons", "anova"], "article_id"=>302205, "categories"=>["Genetics", "Plant Biology"], "users"=>["Federico Martinelli", "Sandra L. Uratsu", "Ute Albrecht", "Russell L. Reagan", "My L. Phu", "Monica Britton", "Vincent Buffalo", "Joseph Fass", "Elizabeth Leicht", "Weixiang Zhao", "Dawei Lin", "Raissa D'Souza", "Cristina E. Davis", "Kim D. Bowman", "Abhaya M. Dandekar"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0038039.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_genes_analyzed_by_quantitative_RT_PCR_including_P_values_for_each_of_three_pairwise_comparisons_from_ANOVA_of_the_expression_data_/302205", "title"=>"List of genes analyzed by quantitative RT-PCR, including P-values for each of three pairwise comparisons from ANOVA of the expression data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-31 00:36:45"}

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