Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during In Vitro Plantlet Growth and Flowering in Amaranthus tricolor L.
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{"title"=>"Transcriptome analysis by illumina high-throughout paired-end sequencing reveals the complexity of differential gene expression during in vitro plantlet growth and flowering in Amaranthus tricolor L", "type"=>"journal", "authors"=>[{"first_name"=>"Shengcai", "last_name"=>"Liu", "scopus_author_id"=>"56239804400"}, {"first_name"=>"Huaqin", "last_name"=>"Kuang", "scopus_author_id"=>"56239583200"}, {"first_name"=>"Zhongxiong", "last_name"=>"Lai", "scopus_author_id"=>"35574141700"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0100919", "pui"=>"373418907", "issn"=>"19326203", "scopus"=>"2-s2.0-84903553208", "sgr"=>"84903553208", "pmid"=>"24963660", "isbn"=>"2012351512000"}, "id"=>"22ee5ccd-5389-3eb4-9995-44ed4a16c61a", "abstract"=>"Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis-based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the process appears to be highly complex in this species.", "link"=>"http://www.mendeley.com/research/transcriptome-analysis-illumina-highthroughout-pairedend-sequencing-reveals-complexity-differential", "reader_count"=>11, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>4, "Arts and Humanities"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1564604"], "description"=>"<p>Length distribution of unigenes identified from <i>Amaranthus tricolor</i> transcriptomes.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "unigenes"], "article_id"=>1082909, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Length_distribution_of_unigenes_identified_from_Amaranthus_tricolor_transcriptomes_/1082909", "title"=>"Length distribution of unigenes identified from <i>Amaranthus tricolor</i> transcriptomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564608"], "description"=>"<p>Gene Ontology (GO) functional classification of genes expressed during <i>Am. tricolor in vitro</i> plantlet growth and flowering.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "ontology", "classification", "genes", "tricolor", "plantlet"], "article_id"=>1082913, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_GO_functional_classification_of_genes_expressed_during_Am_tricolor_in_vitro_plantlet_growth_and_flowering_/1082913", "title"=>"Gene Ontology (GO) functional classification of genes expressed during <i>Am. tricolor in vitro</i> plantlet growth and flowering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564609"], "description"=>"<p>(a) GO functional classification of genes expressed during each developmental stage in <i>Am. tricolor</i>. (b–d) Distribution of expressed genes in each developmental stage associated with the categories of (b) Biological Processes, (c) Cellular Components, and (d) Molecular Function. Developmental stages YSS, ASS, FBS, and FS correspond respectively to young seedling, adult seedling, flower bud, and flowering stages.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics"], "article_id"=>1082914, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_functional_classification_/1082914", "title"=>"GO functional classification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564612"], "description"=>"<p>COG functional classification of genes expressed during <i>Am. tricolor in vitro</i> plantlet growth and flowering.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "classification", "genes", "tricolor", "plantlet"], "article_id"=>1082916, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_functional_classification_of_genes_expressed_during_Am_tricolor_in_vitro_plantlet_growth_and_flowering_/1082916", "title"=>"COG functional classification of genes expressed during <i>Am. tricolor in vitro</i> plantlet growth and flowering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564614"], "description"=>"<p>(from <a href=\"http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map04120&keyword=04120\" target=\"_blank\">http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map04120&keyword=04120</a>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "proteolysis"], "article_id"=>1082918, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ubiquitin_mediated_proteolysis_and_associated_genes_/1082918", "title"=>"Ubiquitin-mediated proteolysis and associated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564616"], "description"=>"<p>(from <a href=\"http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map04712&keyword=04712\" target=\"_blank\">http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map04712&keyword=04712</a>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "circadian-rhythm", "pathways"], "article_id"=>1082920, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plant_circadian_rhythm_pathways_and_genes_/1082920", "title"=>"Plant circadian-rhythm pathways and genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564619"], "description"=>"<p>(from <a href=\"http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map00195&keyword=00195\" target=\"_blank\">http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map00195&keyword=00195</a>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "photosynthesis"], "article_id"=>1082923, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plant_photosynthesis_and_associated_genes_/1082923", "title"=>"Plant photosynthesis and associated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564622"], "description"=>"<p>Venn diagram showing shared and unique unigenes from four developmental stages of <i>Am. tricolor in vitro</i> plantlet growth and flowering.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "diagram", "unigenes", "stages", "tricolor", "plantlet"], "article_id"=>1082926, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_showing_shared_and_unique_unigenes_from_four_developmental_stages_of_Am_tricolor_in_vitro_plantlet_growth_and_flowering_/1082926", "title"=>"Venn diagram showing shared and unique unigenes from four developmental stages of <i>Am. tricolor in vitro</i> plantlet growth and flowering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564626"], "description"=>"<p>(a) Plant circadian rhythm pathway-related unigenes. (b) Ubiquitin-mediated proteolysis pathway-related unigenes. (c–d) Genes related to other or unknown pathways.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "qrt-pcr", "26", "unigenes", "tricolor", "plantlet"], "article_id"=>1082929, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_qRT_PCR_analysis_of_26_candidate_unigenes_during_Am_tricolor_in_vitro_plantlet_growth_and_flowering_/1082929", "title"=>"Results of qRT-PCR analysis of 26 candidate unigenes during <i>Am. tricolor in vitro</i> plantlet growth and flowering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564637"], "description"=>"<p><i>In vitro</i> plantlets of <i>Am. tricolor</i> from four developmental stages, (a) YSS. (b) ASS, (c) FBS, (d) FS.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "plantlets"], "article_id"=>1082939, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vitro_plantlets_of_Am_tricolor_from_four_developmental_stages_a_YSS_b_ASS_c_FBS_d_FS_/1082939", "title"=>"<i>In vitro</i> plantlets of <i>Am. tricolor</i> from four developmental stages, (a) YSS. (b) ASS, (c) FBS, (d) FS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564638"], "description"=>"<p>Summary of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "unigenes", "generated", "transcriptome", "sequencing", "plantlets"], "article_id"=>1082940, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_unigenes_generated_by_transcriptome_sequencing_of_in_vitro_plantlets_of_Am_tricolor_/1082940", "title"=>"Summary of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564639"], "description"=>"<p>Length distribution of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "unigenes", "generated", "transcriptome", "sequencing", "plantlets"], "article_id"=>1082941, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Length_distribution_of_unigenes_generated_by_transcriptome_sequencing_of_in_vitro_plantlets_of_Am_tricolor_/1082941", "title"=>"Length distribution of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564640"], "description"=>"<p>Gene Ontology functional classification of unigenes from <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "ontology", "classification", "unigenes", "plantlets"], "article_id"=>1082942, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_functional_classification_of_unigenes_from_in_vitro_plantlets_of_Am_tricolor_/1082942", "title"=>"Gene Ontology functional classification of unigenes from <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564641"], "description"=>"<p>COG functional classification of <i>Am. tricolor</i> unigenes.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "classification"], "article_id"=>1082943, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_functional_classification_of_Am_tricolor_unigenes_/1082943", "title"=>"COG functional classification of <i>Am. tricolor</i> unigenes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564642"], "description"=>"1<p>YSS  =  young seedling stage; ASS  =  adult seedling stage; FBS  =  flower bud stage; FS  =  flowering stage.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "reads", "generated", "transcriptome", "sequencing", "plantlets"], "article_id"=>1082944, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_summary_of_reads_generated_by_transcriptome_sequencing_of_in_vitro_plantlets_of_Am_tricolor_/1082944", "title"=>"Statistical summary of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564643"], "description"=>"<p>Contigs from assembly of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "reads", "generated", "transcriptome", "sequencing", "plantlets"], "article_id"=>1082945, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contigs_from_assembly_of_reads_generated_by_transcriptome_sequencing_of_in_vitro_plantlets_of_Am_tricolor_/1082945", "title"=>"Contigs from assembly of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564644"], "description"=>"<p>Scaffolds from assembly of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "reads", "generated", "transcriptome", "sequencing", "plantlets"], "article_id"=>1082946, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scaffolds_from_assembly_of_reads_generated_by_transcriptome_sequencing_of_in_vitro_plantlets_of_Am_tricolor_/1082946", "title"=>"Scaffolds from assembly of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564646"], "description"=>"<p>Differentially expressed genes among four developmental stages of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "genes", "stages", "plantlets"], "article_id"=>1082948, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_genes_among_four_developmental_stages_of_in_vitro_plantlets_of_Am_tricolor_/1082948", "title"=>"Differentially expressed genes among four developmental stages of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564647"], "description"=>"<p>Differentially expressed genes during flowering of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "genes", "flowering", "plantlets"], "article_id"=>1082949, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.t009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_genes_during_flowering_of_in_vitro_plantlets_of_Am_tricolor_/1082949", "title"=>"Differentially expressed genes during flowering of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-25 03:08:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1564648", "https://ndownloader.figshare.com/files/1564649"], "description"=>"<div><p><i>Amaranthus tricolor</i> L. is a C<sub>4</sub> plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, <i>Am. tricolor</i> readily bolts and blooms, degrading leaf quality. A preliminary <i>in vitro</i> flowering study demonstrated that the flowering control pathway in <i>Am. tricolor</i> may differ from that of <i>Arabidopsis</i>. Nevertheless, no transcriptome analysis of the flowering process in <i>Amaranthus</i> has been conducted. To study <i>Am. tricolor</i> floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from <i>Am. tricolor</i> at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to <i>in vitro</i> flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for <i>in vitro</i> flowering in <i>Am. tricolor</i>. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from <i>Am. tricolor</i> at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in <i>Am. tricolor</i> growth and development, but the results were somewhat similar to <i>Arabidopsis</i>. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate <i>in vitro</i> plantlet growth and flowering in <i>Am. tricolor</i>, the process appears to be highly complex in this species.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "transcriptome", "illumina", "high-throughout", "paired-end", "sequencing", "reveals", "differential", "plantlet", "flowering"], "article_id"=>1082950, "categories"=>["Biological Sciences"], "users"=>["Shengcai Liu", "Huaqin Kuang", "Zhongxiong Lai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0100919.s001", "https://dx.doi.org/10.1371/journal.pone.0100919.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptome_Analysis_by_Illumina_High_Throughout_Paired_End_Sequencing_Reveals_the_Complexity_of_Differential_Gene_Expression_during_In_Vitro_Plantlet_Growth_and_Flowering_in_Amaranthus_tricolor_L_/1082950", "title"=>"Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during <i>In Vitro</i> Plantlet Growth and Flowering in <i>Amaranthus tricolor</i> L.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-25 03:08:47"}

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Relative Metric

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