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{"title"=>"Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries", "type"=>"journal", "authors"=>[{"first_name"=>"Roberto", "last_name"=>"Sierra", "scopus_author_id"=>"34873538800"}, {"first_name"=>"Luis M.", "last_name"=>"Rodríguez-R", "scopus_author_id"=>"35275742800"}, {"first_name"=>"Diego", "last_name"=>"Chaves", "scopus_author_id"=>"37001627700"}, {"first_name"=>"Andrés", "last_name"=>"Pinzón", "scopus_author_id"=>"8426880400"}, {"first_name"=>"Alejandro", "last_name"=>"Grajales", "scopus_author_id"=>"15062717400"}, {"first_name"=>"Alejandro", "last_name"=>"Rojas", "scopus_author_id"=>"11139163400"}, {"first_name"=>"Gabriel", "last_name"=>"Mutis", "scopus_author_id"=>"37001806600"}, {"first_name"=>"Martha", "last_name"=>"Cárdenas", "scopus_author_id"=>"37001723700"}, {"first_name"=>"Daniel", "last_name"=>"Burbano", "scopus_author_id"=>"57194214236"}, {"first_name"=>"Pedro", "last_name"=>"Jiménez", "scopus_author_id"=>"7103171735"}, {"first_name"=>"Adriana", "last_name"=>"Bernal", "scopus_author_id"=>"7006612034"}, {"first_name"=>"Silvia", "last_name"=>"Restrepo", "scopus_author_id"=>"7003416145"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79952117533", "sgr"=>"79952117533", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0009847", "pmid"=>"20352100", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"368277924"}, "id"=>"2f662179-097e-36c1-bd53-f3dfc847d517", "abstract"=>"BACKGROUND: Phytophthora infestans (Mont.) de Bary causes late blight of potato and tomato, and has a broad host range within the Solanaceae family. Most studies of the Phytophthora--Solanum pathosystem have focused on gene expression in the host and have not analyzed pathogen gene expression in planta. METHODOLOGY/PRINCIPAL FINDINGS: We describe in detail an in silico approach to mine ESTs from inoculated host plants deposited in a database in order to identify particular pathogen sequences associated with disease. We identified candidate effector genes through mining of 22,795 ESTs corresponding to P. infestans cDNA libraries in compatible and incompatible interactions with hosts from the Solanaceae family. CONCLUSIONS/SIGNIFICANCE: We annotated genes of P. infestans expressed in planta associated with late blight using different approaches and assigned putative functions to 373 out of the 501 sequences found in the P. infestans genome draft, including putative secreted proteins, domains associated with pathogenicity and poorly characterized proteins ideal for further experimental studies. Our study provides a methodology for analyzing cDNA libraries and provides an understanding of the plant--oomycete pathosystems that is independent of the host, condition, or type of sample by identifying genes of the pathogen expressed in planta.", "link"=>"http://www.mendeley.com/research/discovery-phytophthora-infestans-genes-expressed-planta-through-mining-cdna-libraries", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>10, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Master"=>6, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>10, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Master"=>6, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>54, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>54}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Colombia"=>2, "United States"=>4, "United Kingdom"=>1, "India"=>2}, "group_count"=>1}

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• http://doi.org/10.1371/journal.pone.0019328
• http://doi.org/10.1128/AEM.03026-15
• http://doi.org/10.1186/1471-2164-12-498
• http://doi.org/10.1016/j.gene.2013.12.009
• http://doi.org/10.1371/journal.pone.0035796
• http://doi.org/10.1007/s11295-014-0698-0

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/856789"], "description"=>"<p>Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.</p>", "links"=>[], "tags"=>["ests", "falling", "gc", "ranges", "403", "had"], "article_id"=>527227, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_ESTs_falling_into_different_GC_content_ranges_among_a_total_of_403_ESTs_that_had_a_hit_against_the_P_infestans_genes_/527227", "title"=>"Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:04:07"}
• {"files"=>["https://ndownloader.figshare.com/files/857178"], "description"=>"<p>The differential abundance (<i>y</i> axis) of predicted CDS to assignable categories (<i>x</i> axis) is shown. KOG categories are as follows (from: <a href=\"http://www.ncbi.nlm.nih.gov/COG/\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/COG/</a>): J, Translation; A, RNA processing and modification; K, Transcription; L, Replication, recombination and repair; B, Chromatin structure and dynamics; D, Cell cycle control, cell division, chromosome partitioning; Y, Nuclear structure; V, Defense mechanisms; T, Signal transduction mechanisms; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; Z, Cytoskeleton; W, Extracellular structures; U, Intracellular trafficking, secretion, and vesicular transport; O, Posttranslational modification, protein turnover, chaperones; C, Energy production and conversion; G, Carbohydrate transport and metabolism; E, Amino acid transport and metabolism; F Nucleotide transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S Function unknown.</p>", "links"=>[], "tags"=>["abundance", "cds", "501", "sequences", "kog"], "article_id"=>527624, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_abundance_of_predicted_CDS_found_in_the_501_selected_sequences_and_the_total_predicted_P_infestans_CDS_based_on_KOG_functional_categories_/527624", "title"=>"Differential abundance of predicted CDS found in the 501 selected sequences and the total predicted <i>P. infestans</i> CDS, based on KOG functional categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:06:16"}
• {"files"=>["https://ndownloader.figshare.com/files/856699"], "description"=>"<p>Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.</p>", "links"=>[], "tags"=>["ests", "contigs", "clustering", "sequences", "downloaded"], "article_id"=>527139, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_ESTs_within_contigs_after_clustering_using_CAP3_the_22_795_sequences_downloaded_from_GenBank_/527139", "title"=>"Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:03:39"}
• {"files"=>["https://ndownloader.figshare.com/files/857275"], "description"=>"<p>GenBank accession numbers and descriptions of the sequences used for this study.</p>", "links"=>[], "tags"=>["accession", "numbers", "descriptions", "sequences"], "article_id"=>527720, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GenBank_accession_numbers_and_descriptions_of_the_sequences_used_for_this_study_/527720", "title"=>"GenBank accession numbers and descriptions of the sequences used for this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:06:49"}
• {"files"=>["https://ndownloader.figshare.com/files/857028"], "description"=>"<p>Blank spaces (i.e. not linked) show sequences annotated by one approach only, one link (connection line) shows it was annotated by two different approaches and so on. The inner circle in a scale of grays shows the bit scores for the BLAST results and the D value and probability S for SignalP results, darker marks show better scores. MF: Molecular Function according to GO categories, BP: Biological Process according to GO categories, CC: Cellular Component according to GO categories, RXLR: BLAST hits against the RXLR database, CRN: Blast hits against the CRN database, and SignalP: secretion peptide results using SignalP.</p>", "links"=>[], "tags"=>["annotation", "signalp", "circos"], "article_id"=>527470, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g005", "stats"=>{"downloads"=>3, "page_views"=>126, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_the_sequence_annotation_using_GO_categories_BLAST_results_and_SignalP_using_the_Circos_software_/527470", "title"=>"Visualization of the sequence annotation using GO categories, BLAST results and SignalP using the Circos software.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:05:29"}
• {"files"=>["https://ndownloader.figshare.com/files/857321"], "description"=>"<p>The sequences identified as belonging to <i>P. infestans</i> but also having a hit against potato and tomato ESTs or any Solanaceae are shown to the right.</p>a<p>((Alignment length * %ID)/Unitig length).</p>", "links"=>[], "tags"=>["resulting", "sequences", "separating", "unitigs", "containing", "pathogen"], "article_id"=>527755, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.t002", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_resulting_candidate_Phytophthora_infestans_sequences_after_separating_12_900_unitigs_containing_pathogen_and_host_sequences_using_different_selection_criteria_/527755", "title"=>"Summary of resulting candidate <i>Phytophthora infestans</i> sequences after separating 12,900 unitigs containing pathogen and host sequences using different selection criteria.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:07:04"}
• {"files"=>["https://ndownloader.figshare.com/files/856911"], "description"=>"<p>12,900 unitigs containing host and pathogen sequences were used to test different approaches to separate both types of sequences. The scheme represents the number of sequences obtained using GC content and a BLAST cut-off e-value combined with different ratio cut-offs: ((Alignment length * %ID)/Unitig length). (a) GC >52%; (b) e-value cut-off of 10⁻¹⁵ (c) e-value cut-off of 10^-15and ratio >50%; (d) e-value cut-off of 10⁻¹⁵ and ratio >60%; (e) e-value cut-off of 10⁻¹⁵ and ratio >70%; (f) e-value cut-off of 10⁻¹⁵ and ratio >80%; (g) e-value cut-off of 10⁻¹⁵ and ratio >90%.</p>", "links"=>[], "tags"=>["sequences", "produces", "notably"], "article_id"=>527353, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Different_criteria_used_to_separate_the_P_infestans_sequences_from_host_sequences_produces_results_that_differ_notably_among_them_/527353", "title"=>"Different criteria used to separate the <i>P. infestans</i> sequences from host sequences produces results that differ notably among them.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:04:46"}
• {"files"=>["https://ndownloader.figshare.com/files/856533"], "description"=>"<p>Main workflow of analysis followed in this study.</p>", "links"=>[], "tags"=>["workflow", "followed"], "article_id"=>526966, "categories"=>["Genetics", "Infectious Diseases", "Biological Sciences"], "users"=>["Roberto Sierra", "Luis M. Rodríguez-R", "Diego Chaves", "Andrés Pinzón", "Alejandro Grajales", "Alejandro Rojas", "Gabriel Mutis", "Martha Cárdenas", "Daniel Burbano", "Pedro Jiménez", "Adriana Bernal", "Silvia Restrepo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009847.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_workflow_of_analysis_followed_in_this_study_/526966", "title"=>"Main workflow of analysis followed in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:02:38"}

PMC Usage Stats | Further Information

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• {"unique-ip"=>"8", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
• {"unique-ip"=>"16", "full-text"=>"11", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
• {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
• {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
• {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
• {"unique-ip"=>"6", "full-text"=>"3", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
• {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
• {"unique-ip"=>"7", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
• {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
• {"unique-ip"=>"15", "full-text"=>"25", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
• {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
• {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
• {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
• {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}

Relative Metric

{"start_date"=>"2010-01-01T00:00:00Z", "end_date"=>"2010-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[288, 576, 733, 867, 984, 1087, 1182, 1267, 1346, 1424, 1501, 1577, 1646, 1711, 1778, 1841, 1908, 1970, 2034, 2102, 2162, 2227, 2296, 2359, 2422, 2482, 2550, 2610, 2679, 2747, 2820, 2887, 2955, 3009, 3067, 3130, 3200, 3257, 3322, 3379, 3443, 3507, 3571, 3632, 3683, 3753, 3822, 3877]}, {"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[289, 556, 715, 853, 962, 1053, 1146, 1230, 1307, 1373, 1443, 1524, 1582, 1669, 1720, 1810, 1876, 1929, 2012, 2087, 2168, 2241, 2320, 2385, 2469, 2534, 2605, 2681, 2745, 2812, 2861, 2909, 2988, 3068, 3166, 3213, 3266, 3346, 3419, 3508, 3566, 3631, 3692, 3746, 3809, 3882, 3964, 4024, 4100]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[283, 565, 720, 852, 970, 1070, 1168, 1258, 1336, 1411, 1487, 1571, 1640, 1709, 1776, 1843, 1906, 1969, 2031, 2086, 2152, 2221, 2286, 2361, 2419, 2480, 2543, 2598, 2665, 2731, 2802, 2868, 2932, 2996, 3053, 3114, 3169, 3232, 3289, 3355, 3413, 3473, 3530, 3595, 3648, 3711, 3764, 3810, 3863]}]}

F1000Prime