Transcriptome Analysis of Catharanthus roseus for Gene Discovery and Expression Profiling
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{"title"=>"Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling", "type"=>"journal", "authors"=>[{"first_name"=>"Mohit", "last_name"=>"Verma", "scopus_author_id"=>"56048086900"}, {"first_name"=>"Rajesh", "last_name"=>"Ghangal", "scopus_author_id"=>"35784182300"}, {"first_name"=>"Raghvendra", "last_name"=>"Sharma", "scopus_author_id"=>"55794634500"}, {"first_name"=>"Alok K.", "last_name"=>"Sinha", "scopus_author_id"=>"7403680314"}, {"first_name"=>"Mukesh", "last_name"=>"Jain", "scopus_author_id"=>"55584797084"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25072156", "doi"=>"10.1371/journal.pone.0103583", "sgr"=>"84904991638", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84904991638", "issn"=>"19326203", "pui"=>"373644925"}, "id"=>"7b209ac9-fc3b-31b6-9040-42879686e83c", "abstract"=>"The medicinal plant, Catharanthus roseus, accumulates wide range of terpenoid indole alkaloids, which are well documented therapeutic agents. In this study, deep transcriptome sequencing of C. roseus was carried out to identify the pathways and enzymes (genes) involved in biosynthesis of these compounds. About 343 million reads were generated from different tissues (leaf, flower and root) of C. roseus using Illumina platform. Optimization of de novo assembly involving a two-step process resulted in a total of 59,220 unique transcripts with an average length of 1284 bp. Comprehensive functional annotation and gene ontology (GO) analysis revealed the representation of many genes involved in different biological processes and molecular functions. In total, 65% of C. roseus transcripts showed homology with sequences available in various public repositories, while remaining 35% unigenes may be considered as C. roseus specific. In silico analysis revealed presence of 11,620 genic simple sequence repeats (excluding mono-nucleotide repeats) and 1820 transcription factor encoding genes in C. roseus transcriptome. Expression analysis showed roots and leaves to be actively participating in bisindole alkaloid production with clear indication that enzymes involved in pathway of vindoline and vinblastine biosynthesis are restricted to aerial tissues. Such large-scale transcriptome study provides a rich source for understanding plant-specialized metabolism, and is expected to promote research towards production of plant-derived pharmaceuticals.", "link"=>"http://www.mendeley.com/research/transcriptome-analysis-catharanthus-roseus-gene-discovery-expression-profiling-1", "reader_count"=>40, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>10, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>10, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>28, "Chemical Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Serbia and Montenegro"=>1, "India"=>3}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1613185"], "description"=>"<p>(A) Distribution of SSRs in different classes (B) Frequency of most common SSRs motifs is shown by bar graph.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics", "repeats"], "article_id"=>1120896, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103583.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_simple_sequence_repeats_SSRs_in_C_roseus_transcriptome_/1120896", "title"=>"Identification of simple sequence repeats (SSRs) in <i>C. roseus</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-29 02:53:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1613188"], "description"=>"1<p>Similarity search was done against TAIR10 proteome.</p>2<p>Assembly generated by merging best k-mer with MPGR transcriptome using TGICL.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics", "illumina"], "article_id"=>1120899, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103583.t001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assembly_optimization_validation_of_Illumina_data_of_C_roseus_/1120899", "title"=>"Assembly optimization/validation of Illumina data of <i>C. roseus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-29 02:53:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1613187"], "description"=>"<p>(A) Vindoline biosynthetic pathway showing important enzymes involved in different reactions. The IDs of <i>C. roseus</i> transcript encoding for the respective enzymes are also indicated. The important intermediates have been highlighted in bold font. (B) Heat-map showing expression patterns of TIA genes in different tissues and treatment. The scale at the bottom of each study represents log<sub>2</sub> value of RPKM. Transcript IDs are given at left side and their putative annotation is on right side. (C) The correlation of gene expression results obtained from RNA-seq and real time RT-PCR analysis (D) Heat-map showing expression pattern of TF encoding genes in different tissues and treatment. The scale at the bottom of each study represents log<sub>2</sub> value of RPKM. Transcript IDs are given at left side and their putative annotation is on right side.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics", "patterns", "transcripts", "tia"], "article_id"=>1120898, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103583.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_patterns_of_transcripts_involved_in_TIA_biosynthesis_/1120898", "title"=>"Expression patterns of transcripts involved in TIA biosynthesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-29 02:53:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1613190", "https://ndownloader.figshare.com/files/1613191", "https://ndownloader.figshare.com/files/1613192", "https://ndownloader.figshare.com/files/1613193", "https://ndownloader.figshare.com/files/1613194", "https://ndownloader.figshare.com/files/1613195", "https://ndownloader.figshare.com/files/1613196", "https://ndownloader.figshare.com/files/1613197", "https://ndownloader.figshare.com/files/1613198", "https://ndownloader.figshare.com/files/1613199", "https://ndownloader.figshare.com/files/1613200"], "description"=>"<div><p>The medicinal plant, <i>Catharanthus roseus</i>, accumulates wide range of terpenoid indole alkaloids, which are well documented therapeutic agents. In this study, deep transcriptome sequencing of <i>C. roseus</i> was carried out to identify the pathways and enzymes (genes) involved in biosynthesis of these compounds. About 343 million reads were generated from different tissues (leaf, flower and root) of <i>C. roseus</i> using Illumina platform. Optimization of <i>de novo</i> assembly involving a two-step process resulted in a total of 59,220 unique transcripts with an average length of 1284 bp. Comprehensive functional annotation and gene ontology (GO) analysis revealed the representation of many genes involved in different biological processes and molecular functions. In total, 65% of <i>C. roseus</i> transcripts showed homology with sequences available in various public repositories, while remaining 35% unigenes may be considered as <i>C. roseus</i> specific. <i>In silico</i> analysis revealed presence of 11,620 genic simple sequence repeats (excluding mono-nucleotide repeats) and 1820 transcription factor encoding genes in <i>C. roseus</i> transcriptome. Expression analysis showed roots and leaves to be actively participating in bisindole alkaloid production with clear indication that enzymes involved in pathway of vindoline and vinblastine biosynthesis are restricted to aerial tissues. Such large-scale transcriptome study provides a rich source for understanding plant-specialized metabolism, and is expected to promote research towards production of plant-derived pharmaceuticals.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics", "transcriptome", "profiling"], "article_id"=>1120901, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0103583.s001", "https://dx.doi.org/10.1371/journal.pone.0103583.s002", "https://dx.doi.org/10.1371/journal.pone.0103583.s003", "https://dx.doi.org/10.1371/journal.pone.0103583.s004", "https://dx.doi.org/10.1371/journal.pone.0103583.s005", "https://dx.doi.org/10.1371/journal.pone.0103583.s006", "https://dx.doi.org/10.1371/journal.pone.0103583.s007", "https://dx.doi.org/10.1371/journal.pone.0103583.s008", "https://dx.doi.org/10.1371/journal.pone.0103583.s009", "https://dx.doi.org/10.1371/journal.pone.0103583.s010", "https://dx.doi.org/10.1371/journal.pone.0103583.s011"], "stats"=>{"downloads"=>7, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptome_Analysis_of_Catharanthus_roseus_for_Gene_Discovery_and_Expression_Profiling/1120901", "title"=>"Transcriptome Analysis of <i>Catharanthus roseus</i> for Gene Discovery and Expression Profiling", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-29 02:53:09"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1613186"], "description"=>"<p>(A) Number of differentially expressed genes in different tissues in pairwise comparisons. Number of up-regulated genes are in bold, while down-regulated are in normal font. (B) Venn diagram showing number of up- and down-regulated (in parentheses) genes in leaf and root tissues as compared to flower. Asterisk represents genes up-regulated in one tissue and down-regulated in another tissue. (C) Heat-map showing expression patterns of differentially up-regulated TF encoding genes in different tissues. The scale at the bottom represents log<sub>2</sub> fold change. (D) Graphical view showing GO terms associated with biological process enriched in up-regulated genes of leaf. The GO enrichment was performed using BiNGO. Node size is proportional to the number of genes in each category and shades represent the scale denoting significance level (white- no significant difference).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics"], "article_id"=>1120897, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103583.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_analysis_of_C_roseus_transcriptome_/1120897", "title"=>"Differential expression analysis of <i>C. roseus</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-29 02:53:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1613184"], "description"=>"<p>Number of transcripts representing different transcription factor families in <i>C. roseus</i> transcriptome.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "next-generation sequencing", "Gene ontologies", "Plant science", "Plant biotechnology", "Plant genomics", "transcripts", "transcription"], "article_id"=>1120895, "categories"=>["Biological Sciences"], "users"=>["Mohit Verma", "Rajesh Ghangal", "Raghvendra Sharma", "Alok K. Sinha", "Mukesh Jain"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103583.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_transcripts_representing_different_transcription_factor_families_in_C_roseus_transcriptome_/1120895", "title"=>"Number of transcripts representing different transcription factor families in <i>C. roseus</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-29 02:53:09"}

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  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"20", "full-text"=>"24", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"17", "full-text"=>"15", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"11", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"16", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"11", "cited-by"=>"1", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"17", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[278, 438]}]}
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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-08-27 19:06:17 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0103583)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'