De novo Assembly and Characterization of the Global Transcriptome for Rhyacionia leptotubula Using Illumina Paired-End Sequencing
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{"title"=>"De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using illumina paired-end sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Jia Ying", "last_name"=>"Zhu", "scopus_author_id"=>"36524423300"}, {"first_name"=>"Yong He", "last_name"=>"Li", "scopus_author_id"=>"55384230700"}, {"first_name"=>"Song", "last_name"=>"Yang", "scopus_author_id"=>"56386294600"}, {"first_name"=>"Qin Wen", "last_name"=>"Li", "scopus_author_id"=>"56143086800"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24278383", "sgr"=>"84896738509", "doi"=>"10.1371/journal.pone.0081096", "scopus"=>"2-s2.0-84896738509", "pui"=>"372425689", "issn"=>"19326203"}, "id"=>"4ffb8eb3-d4f9-3220-95d8-b959728f4066", "abstract"=>"BACKGROUND: The pine tip moth, Rhyacionia leptotubula (Lepidoptera: Tortricidae) is one of the most destructive forestry pests in Yunnan Province, China. Despite its importance, less is known regarding all aspects of this pest. Understanding the genetic information of it is essential for exploring the specific traits at the molecular level. Thus, we here sequenced the transcriptome of R. leptotubula with high-throughput Illumina sequencing.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: In a single run, more than 60 million sequencing reads were generated. De novo assembling was performed to generate a collection of 46,910 unigenes with mean length of 642 bp. Based on Blastx search with an E-value cut-off of 10(-5), 22,581 unigenes showed significant similarities to known proteins from National Center for Biotechnology Information (NCBI) non-redundant (Nr) protein database. Of these annotated unigenes, 10,360, 6,937 and 13,894 were assigned to Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 5,926 unigenes were annotated with domain similarity derived functional information, of which 55 and 39 unigenes respectively encoding the insecticide resistance related enzymes, cytochrome P450 and carboxylesterase. Using the transcriptome data, 47 unigenes belonging to the typical \"stress\" genes of heat shock protein (Hsp) family were retrieved. Furthermore, 1,450 simple sequence repeats (SSRs) were detected; 3.09% of the unigenes contained SSRs. Large numbers of SSR primer pairs were designed and out of randomly verified primer pairs 80% were successfully yielded amplicons.\\n\\nCONCLUSIONS/SIGNIFICANCE: A large of putative R. leptotubula transcript sequences has been obtained from the deep sequencing, which extensively increases the comprehensive and integrated genomic resources of this pest. This large-scale transcriptome dataset will be an important information platform for promoting our investigation of the molecular mechanisms from various aspects in this species.", "link"=>"http://www.mendeley.com/research/novo-assembly-characterization-global-transcriptome-rhyacionia-leptotubula-using-illumina-pairedend", "reader_count"=>16, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>9, "Neuroscience"=>2, "Veterinary Science and Veterinary Medicine"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Spain"=>1, "India"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291864/Figure_1.tif"], "description"=>"<p>(A) E-value distribution of BLAST hits for each unigene with a cutoff E-value of 1E-5 in the Nr database. (B) Similarity distribution. (C) Species distribution. The distribution is shown as a percentage of the total BLAST hits for each unigene with a cutoff E-value of 1E-5 in the Nr database.</p>", "links"=>[], "tags"=>["unigenes", "nr"], "article_id"=>859522, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Characteristics_of_similarity_search_of_unigenes_against_Nr_databases_/859522", "title"=>"Characteristics of similarity search of unigenes against Nr databases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291865/Figure_2.tif"], "description"=>"<p>In total, 15,082 unigenes were grouped into 24 COG classifications.</p>", "links"=>[], "tags"=>["cog"], "article_id"=>859523, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Histogram_presentation_of_COG_classification_/859523", "title"=>"Histogram presentation of COG classification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291870/Figure_3.tif"], "description"=>"<p>Top 27 Pfam domains predcted in translated unigenes.</p>", "links"=>[], "tags"=>["27", "pfam", "domains", "predcted", "translated"], "article_id"=>859528, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Top_27_Pfam_domains_predcted_in_translated_unigenes_/859528", "title"=>"Top 27 Pfam domains predcted in translated unigenes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291871/Figure_4.tif"], "description"=>"<p>Analyses were performed using only sequences predicted to encode complete ORFs. The tree is a 50% consensus tree. Abbreviations are as follows: Api, <i>Acyrthosiphon pisum</i>; <i>Ame, Apis mellifera</i>; Cqu, <i>Culex quinquefasciatus</i>; Dpl, <i>Danaus plexippus</i>; Foc, <i>Frankliniella occidentalis</i>; Lmi, <i>Locusta migratoria</i>; Lhe, <i>Lygus hesperus</i>; Phu, <i>Pediculus humanus corporis</i>; Rle, <i>Rhyacionia leptotubula</i>; Tca, <i>Tribolium castaneum</i>.</p>", "links"=>[], "tags"=>["shoch", "protens"], "article_id"=>859529, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Phylogenetic_analysis_of_heat_shoch_protens_from_different_insects_/859529", "title"=>"Phylogenetic analysis of heat shoch protens from different insects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291873/Figure_5.tif"], "description"=>"<p>The frequency of main motif types was displayed.</p>", "links"=>[], "tags"=>["ssrs", "motif"], "article_id"=>859531, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Frequency_distribution_of_SSRs_based_on_motif_types_/859531", "title"=>"Frequency distribution of SSRs based on motif types.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291874/Table_4.xls"], "description"=>"<p>Statistics of SSR searching results.</p>", "links"=>[], "tags"=>["ssr", "searching"], "article_id"=>859532, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Statistics_of_SSR_searching_results_/859532", "title"=>"Statistics of SSR searching results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291875/Table_5.xls"], "description"=>"<p>Distribution of SSRs based on the number of repeat units.</p>", "links"=>[], "tags"=>["ssrs"], "article_id"=>859533, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Distribution_of_SSRs_based_on_the_number_of_repeat_units_/859533", "title"=>"Distribution of SSRs based on the number of repeat units.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291876/Table_2.xls"], "description"=>"<p>A total of 6,937 unigenes were annotated by three categories: biological process,cellular component, and molecular function. The number and ratio of unigenes assigned to level 2 GO terms were shown. Percent of unigenes represents each class comprising in all unigenes assigned into each ontology category.</p>", "links"=>[], "tags"=>["classifications", "assembled"], "article_id"=>859534, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_GO_classifications_of_assembled_unigenes_/859534", "title"=>"GO classifications of assembled unigenes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291877/Table_3.xls"], "description"=>"<p>Putatively identified heat shock protein (Hsp) genes.</p>", "links"=>[], "tags"=>[], "article_id"=>859535, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Putatively_identified_heat_shock_protein_Hsp_genes_/859535", "title"=>"Putatively identified heat shock protein (Hsp) genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291878/Table_1.xls"], "description"=>"<p>Summary of assembled contigs and unigenes.</p>", "links"=>[], "tags"=>["assembled", "contigs"], "article_id"=>859536, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Summary_of_assembled_contigs_and_unigenes_/859536", "title"=>"Summary of assembled contigs and unigenes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-21 03:46:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291882/Figure_S1.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291883/Figure_S2.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291884/Figure_S3.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291885/Figure_S4.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291886/Figure_S5.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291887/Figure_S6.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291888/Figure_S7.ppt", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291889/Table_S1.xls", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291891/Table_S2.doc", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291892/Table_S3.xls", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291893/Table_S4.xls", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291894/Table_S5.xls", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1291895/Table_S6.xls"], "description"=>"<div><p>Background</p><p>The pine tip moth, <i>Rhyacionia leptotubula</i> (Lepidoptera: Tortricidae) is one of the most destructive forestry pests in Yunnan Province, China. Despite its importance, less is known regarding all aspects of this pest. Understanding the genetic information of it is essential for exploring the specific traits at the molecular level. Thus, we here sequenced the transcriptome of <i>R. leptotubula</i> with high-throughput Illumina sequencing.</p><p>Methodology/Principal Findings</p><p>In a single run, more than 60 million sequencing reads were generated. <i>De novo</i> assembling was performed to generate a collection of 46,910 unigenes with mean length of 642 bp. Based on Blastx search with an E-value cut-off of 10<sup>−5</sup>, 22,581 unigenes showed significant similarities to known proteins from National Center for Biotechnology Information (NCBI) non-redundant (Nr) protein database. Of these annotated unigenes, 10,360, 6,937 and 13,894 were assigned to Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 5,926 unigenes were annotated with domain similarity derived functional information, of which 55 and 39 unigenes respectively encoding the insecticide resistance related enzymes, cytochrome P450 and carboxylesterase. Using the transcriptome data, 47 unigenes belonging to the typical “stress” genes of heat shock protein (Hsp) family were retrieved. Furthermore, 1,450 simple sequence repeats (SSRs) were detected; 3.09% of the unigenes contained SSRs. Large numbers of SSR primer pairs were designed and out of randomly verified primer pairs 80% were successfully yielded amplicons.</p><p>Conclusions/Significance</p><p>A large of putative <i>R. leptotubula</i> transcript sequences has been obtained from the deep sequencing, which extensively increases the comprehensive and integrated genomic resources of this pest. This large-scale transcriptome dataset will be an important information platform for promoting our investigation of the molecular mechanisms from various aspects in this species.</p></div>", "links"=>[], "tags"=>["characterization", "transcriptome", "illumina", "paired-end", "sequencing"], "article_id"=>859540, "categories"=>["Biological Sciences"], "users"=>["Jia-Ying Zhu", "Yong-He Li", "Song Yang", "Qin-Wen Li"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0081096"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_De_novo_Assembly_and_Characterization_of_the_Global_Transcriptome_for_Rhyacionia_leptotubula_Using_Illumina_Paired_End_Sequencing/859540", "title"=>"<i>De novo</i> Assembly and Characterization of the Global Transcriptome for <i>Rhyacionia leptotubula</i> Using Illumina Paired-End Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-21 03:46:29"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[272, 472, 600, 713, 815, 911, 1004, 1094, 1185, 1273, 1358, 1441]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}]}
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