Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications
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{"title"=>"Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: Development and applications", "type"=>"journal", "authors"=>[{"first_name"=>"Himabindu", "last_name"=>"Kudapa", "scopus_author_id"=>"38361662200"}, {"first_name"=>"Sarwar", "last_name"=>"Azam", "scopus_author_id"=>"54889077400"}, {"first_name"=>"Andrew G.", "last_name"=>"Sharpe", "scopus_author_id"=>"7103330477"}, {"first_name"=>"Bunyamin", "last_name"=>"Taran", "scopus_author_id"=>"57190242372"}, {"first_name"=>"Rong", "last_name"=>"Li", "scopus_author_id"=>"55491312900"}, {"first_name"=>"Benjamin", "last_name"=>"Deonovic", "scopus_author_id"=>"56149614000"}, {"first_name"=>"Connor", "last_name"=>"Cameron", "scopus_author_id"=>"55889184000"}, {"first_name"=>"Andrew D.", "last_name"=>"Farmer", "scopus_author_id"=>"34769861100"}, {"first_name"=>"Steven B.", "last_name"=>"Cannon", "scopus_author_id"=>"26643308900"}, {"first_name"=>"Rajeev K.", "last_name"=>"Varshney", "scopus_author_id"=>"7006648166"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84898058216", "sgr"=>"84898058216", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0086039", "pmid"=>"24465857", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"373023156"}, "id"=>"e1de824d-66a2-33b3-93f4-2496a7b0c873", "abstract"=>"A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.", "link"=>"http://www.mendeley.com/research/comprehensive-transcriptome-assembly-chickpea-cicer-arietinum-l-using-sanger-next-generation-sequenc", "reader_count"=>49, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>33, "Medicine and Dentistry"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>33}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>1, "United Kingdom"=>1, "Chile"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1358458", "https://ndownloader.figshare.com/files/1358460", "https://ndownloader.figshare.com/files/1358461"], "description"=>"<div><p>A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as <i><u>C</u>icer <u>a</u>rietinum</i><u>T</u>ranscriptome <u>A</u>ssembly version 2 (CaTA v2, available at <a href=\"http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201\" target=\"_blank\">http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201</a>), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - <i>Medicago</i>, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the <i>Medicago</i> genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.</p></div>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "transcriptome", "chickpea", "sanger", "sequencing", "applications"], "article_id"=>910619, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0086039.s001", "https://dx.doi.org/10.1371/journal.pone.0086039.s002", "https://dx.doi.org/10.1371/journal.pone.0086039.s003"], "stats"=>{"downloads"=>6, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comprehensive_Transcriptome_Assembly_of_Chickpea_Cicer_arietinum_L_Using_Sanger_and_Next_Generation_Sequencing_Platforms_Development_and_Applications/910619", "title"=>"Comprehensive Transcriptome Assembly of Chickpea (<i>Cicer arietinum</i> L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358452"], "description"=>"<p>Correspondences of chickpea genic molecular markers to <i>Medicago</i>.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "chickpea", "genic", "molecular", "markers"], "article_id"=>910613, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correspondences_of_chickpea_genic_molecular_markers_to_Medicago_/910613", "title"=>"Correspondences of chickpea genic molecular markers to <i>Medicago</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358437"], "description"=>"<p>Based on conserved domain annotation, Transcript Assembly Contigs (TACs) showing significant annotation to transcription factors were classified.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "chickpea", "transcripts", "transcription"], "article_id"=>910598, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.g003", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_chickpea_transcripts_in_different_transcription_factor_TF_families_/910598", "title"=>"Distribution of chickpea transcripts in different transcription factor (TF) families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358433"], "description"=>"<p>Chickpea TACs representing the distribution of genes based on their annotations to terms in the GO were categorized hierarchically according to three principal gene ontologies, viz. biological processes, molecular functions and cellular components. The number of TACs representing each subcategory is shown in Y-axis.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "categorization", "chickpea", "transcript", "contigs", "cata"], "article_id"=>910594, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.g001", "stats"=>{"downloads"=>4, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_categorization_of_chickpea_Transcript_Assembly_Contigs_TACs_of_the_CaTA_v2_/910594", "title"=>"Functional categorization of chickpea Transcript Assembly Contigs (TACs) of the CaTA v2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358446"], "description"=>"<p>Distribution ISRs on chickpea contigs.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "isrs", "chickpea"], "article_id"=>910607, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t008", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_ISRs_on_chickpea_contigs_/910607", "title"=>"Distribution ISRs on chickpea contigs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358448"], "description"=>"<p>Comparative analysis of chickpea transcriptome assemblies.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "chickpea", "transcriptome"], "article_id"=>910608, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t002", "stats"=>{"downloads"=>5, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_chickpea_transcriptome_assemblies_/910608", "title"=>"Comparative analysis of chickpea transcriptome assemblies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358445"], "description"=>"<p>This image is from Legume Information System (LIS) GBrowse viewer at <a href=\"http://medtr.comparative-legumes.org/gb2/gbrowse/3.5.1/\" target=\"_blank\">http://medtr.comparative-legumes.org/gb2/gbrowse/3.5.1/</a>, shows 1 Mb (17,648,842.18,648,841 of <i>Medicago</i>, chromosome Mt1). Red: There was at least one additional reported CaTA v2 alignment Green: There were no other reported alignments.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "chickpea", "markers", "isr", "genome"], "article_id"=>910606, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.g004", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_sample_view_of_chickpea_TACs_markers_and_candidate_ISR_markers_onto_Medicago_Genome_sequence_/910606", "title"=>"A sample view of chickpea TACs, markers and candidate ISR markers onto <i>Medicago</i> Genome sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358456"], "description"=>"<p>Identification of simple sequence repeats: their distribution and primer design for chickpea genetics and breeding applications.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "primer", "chickpea", "breeding"], "article_id"=>910617, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t005", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_simple_sequence_repeats_their_distribution_and_primer_design_for_chickpea_genetics_and_breeding_applications_/910617", "title"=>"Identification of simple sequence repeats: their distribution and primer design for chickpea genetics and breeding applications.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358454"], "description"=>"<p>Distribution of ISRs on chickpea linkage groups.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "isrs", "chickpea", "linkage"], "article_id"=>910615, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_ISRs_on_chickpea_linkage_groups_/910615", "title"=>"Distribution of ISRs on chickpea linkage groups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358455"], "description"=>"<p>Multiple mapping of CaTA v2 onto <i>Medicago</i> genome.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "cata", "v2"], "article_id"=>910616, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_mapping_of_CaTA_v2_onto_Medicago_genome_/910616", "title"=>"Multiple mapping of CaTA v2 onto <i>Medicago</i> genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358451"], "description"=>"1<p>Tissues collected: a) 2-week old leaf, b) stem before flowering, c) 1-week-old etiolated seedling, d) mixed flower stages and e) developing seed at mixed stages.</p>*<p>NIPGR- National Institute of Plant Genome Research, India; ICRISAT- International Crops Research Institute for the Semi-Arid Tropics, India; JCVI- J. Craig Venter Institute, USA; NRC- National Research Council Canada.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "ngs", "sanger", "sequencing", "datasets", "chickpea", "transcriptome"], "article_id"=>910611, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t001", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_on_NGS_FLX_454_and_Illumina_and_Sanger_sequencing_datasets_used_for_developing_comprehensive_chickpea_transcriptome_assembly_CaTA_v2_/910611", "title"=>"Details on NGS (FLX/454 and Illumina) and Sanger sequencing datasets used for developing comprehensive chickpea transcriptome assembly (CaTA v2).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358435"], "description"=>"<p>The graph displays the proportion of genes belonging to each enzyme class.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "classification", "chickpea", "transcript", "contigs", "enzyme"], "article_id"=>910596, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.g002", "stats"=>{"downloads"=>2, "page_views"=>276, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enzyme_classification_of_chickpea_Transcript_Assembly_Contigs_TACs_among_the_six_enzyme_classes_/910596", "title"=>"Enzyme classification of chickpea Transcript Assembly Contigs (TACs) among the six enzyme classes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-23 03:56:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1358449"], "description"=>"<p>Mapping of chickpea TACs onto <i>Medicago</i> genome.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "biotechnology", "Computational biology", "genomics", "Genome analysis tools", "Sequence assembly tools", "transcriptomes", "Sequence analysis", "developmental biology", "genetics", "Genome databases", "Sequence databases", "Model organisms", "Plant science", "Plant biotechnology", "Plant genetics", "Plant genomics", "plants", "chickpea", "tacs"], "article_id"=>910610, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Himabindu Kudapa", "Sarwar Azam", "Andrew G. Sharpe", "Bunyamin Taran", "Rong Li", "Benjamin Deonovic", "Connor Cameron", "Andrew D. Farmer", "Steven B. Cannon", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086039.t003", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mapping_of_chickpea_TACs_onto_Medicago_genome_/910610", "title"=>"Mapping of chickpea TACs onto <i>Medicago</i> genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-23 03:56:16"}

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