Transcript Profiling Reveals Auxin and Cytokinin Signaling Pathways and Transcription Regulation during In Vitro Organogenesis of Ramie (Boehmeria nivea L. Gaud)
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{"title"=>"Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of ramie (boehmeria nivea l. Gaud)", "type"=>"journal", "authors"=>[{"first_name"=>"Xing", "last_name"=>"Huang", "scopus_author_id"=>"56173942200"}, {"first_name"=>"Jie", "last_name"=>"Chen", "scopus_author_id"=>"56021260200"}, {"first_name"=>"Yaning", "last_name"=>"Bao", "scopus_author_id"=>"56431957700"}, {"first_name"=>"Lijun", "last_name"=>"Liu", "scopus_author_id"=>"55715181400"}, {"first_name"=>"Hui", "last_name"=>"Jiang", "scopus_author_id"=>"57199202495"}, {"first_name"=>"Xia", "last_name"=>"An", "scopus_author_id"=>"56019518600"}, {"first_name"=>"Lunjin", "last_name"=>"Dai", "scopus_author_id"=>"56431935600"}, {"first_name"=>"Bo", "last_name"=>"Wang", "scopus_author_id"=>"56926926100"}, {"first_name"=>"Dingxiang", "last_name"=>"Peng", "scopus_author_id"=>"24598214700"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"600550007", "doi"=>"10.1371/journal.pone.0113768", "sgr"=>"84913596510", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25415356", "scopus"=>"2-s2.0-84913596510"}, "id"=>"cd7415ca-4ca7-3d6d-b8ca-44e83ac43dee", "abstract"=>"In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.", "link"=>"http://www.mendeley.com/research/transcript-profiling-reveals-auxin-cytokinin-signaling-pathways-transcription-regulation-during-vitr", "reader_count"=>21, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>16, "Arts and Humanities"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Slovenia"=>1, "Slovakia"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1804137"], "description"=>"<p>*Subgroup of zinc finger family.</p><p>Regulated transcription factors during in vitro organogenesis.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249342, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.t001", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulated_transcription_factors_during_in_vitro_organogenesis_/1249342", "title"=>"Regulated transcription factors during in vitro organogenesis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804134"], "description"=>"<p>The relative expression levels were obtained by RNA-Seq after taking logarithmic transformations of RPKM.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249339, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g006", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_genes_related_to_auxin_and_cytokinin_signaling_/1249339", "title"=>"Differentially expressed genes related to auxin and cytokinin signaling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804133"], "description"=>"<p>The relative expression level was obtained after taking equation and logarithmic transformations of RPKM.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249338, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g005", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_genes_during_in_vitro_organogenesis_were_clustered_by_the_k_Means_method_which_is_based_on_their_expression_modulation_/1249338", "title"=>"Differentially expressed genes during in vitro organogenesis were clustered by the k-Means method, which is based on their expression modulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804136"], "description"=>"<p>Comparison of expression profiles of 37 phytohormone related genes by qRT-PCR and RNA-Seq in ramie cultivar H5 (A). Comparisons of expression profiles of auxin (B) and cytokinin (C) related genes in H5 (blue), DZ (red) and Arabidopsis (A.TH, purple). The expression data of Arabidopsis genes was obtained from a published article <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113768#pone.0113768-Che1\" target=\"_blank\">[5]</a>.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249341, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g008", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_qRT_PCR_with_DGE_data_of_ramie_and_microarray_data_of_Arabidopsis_/1249341", "title"=>"Comparisons of qRT-PCR with DGE data of ramie and microarray data of Arabidopsis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804135"], "description"=>"<p>The relative expression level was obtained by qRT-PCR after logarithmic transformation of the data. The correlation coefficient (R) was calculated by SPSS.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249340, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g007", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_pattern_and_correlations_for_auxin_and_cytokinin_related_genes_in_two_ramie_cultivars_H5_and_DZ_/1249340", "title"=>"Expression pattern and correlations for auxin and cytokinin related genes in two ramie cultivars, H5 and DZ.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804132"], "description"=>"<p>Differential expression was calculated by comparison with the pre-induction stage (control) (A) and with the prior sampling point (B). The DEGs were identified using DESeq. The Venn diagram shows specifically or commonly expressed DEGs during the callus and shoot stages (C).</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249337, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g004", "stats"=>{"downloads"=>3, "page_views"=>64, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histogram_and_Venn_diagram_of_DEGs_during_in_vitro_organogenesis_/1249337", "title"=>"Histogram and Venn diagram of DEGs during in vitro organogenesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804130"], "description"=>"<p>The results are classified into three main categories: biological process, cellular component and molecular function.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249335, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_classifications_for_the_assembled_unigenes_/1249335", "title"=>"Gene Ontology classifications for the assembled unigenes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804131"], "description"=>"<p>Distribution of the assembled unigenes across the KOG categories.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249336, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_assembled_unigenes_across_the_KOG_categories_/1249336", "title"=>"Distribution of the assembled unigenes across the KOG categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804129"], "description"=>"<p>Petiole explants from H5 (A–E) and DZ (F–J) were sampled for RNA extraction at five sequential time points. They were incubated on MS medium containing TDZ (0.25 mg/L) and NAA (0.06 mg/L) for 0 (A, F), 4 (B, G), 14 (C, H), 28 (D, I) and 35 (E, J) days.</p>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249334, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113768.g001", "stats"=>{"downloads"=>5, "page_views"=>86, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_observation_of_H5_and_DZ_at_different_time_points_during_in_vitro_organogenesis_/1249334", "title"=>"Morphological observation of H5 and DZ at different time points during in vitro organogenesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-21 03:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1804138", "https://ndownloader.figshare.com/files/1804139", "https://ndownloader.figshare.com/files/1804140", "https://ndownloader.figshare.com/files/1804141", "https://ndownloader.figshare.com/files/1804142", "https://ndownloader.figshare.com/files/1804143", "https://ndownloader.figshare.com/files/1804144", "https://ndownloader.figshare.com/files/1804145", "https://ndownloader.figshare.com/files/1804146", "https://ndownloader.figshare.com/files/1804147"], "description"=>"<div><p><i>In vitro</i> organogenesis, one of the most common pathways leading to <i>in vitro</i> plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis <i>in vitro</i> organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie <i>in vitro</i> organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. <i>De novo</i> assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of <i>in vitro</i> organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the <i>in vitro</i> organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.</p></div>", "links"=>[], "tags"=>["Genomes Pathway database", "organogenesi", "reference transcriptome library", "ramie regeneration system", "deg", "Boehmeria nivea L", "dge", "expression", "ramie cultivars", "cytokinin", "future phytohormone research", "Cytokinin Signaling Pathways", "auxin"], "article_id"=>1249343, "categories"=>["Uncategorised"], "users"=>["Xing Huang", "Jie Chen", "Yaning Bao", "Lijun Liu", "Hui Jiang", "Xia An", "Lunjin Dai", "Bo Wang", "Dingxiang Peng"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0113768.s001", "https://dx.doi.org/10.1371/journal.pone.0113768.s002", "https://dx.doi.org/10.1371/journal.pone.0113768.s003", "https://dx.doi.org/10.1371/journal.pone.0113768.s004", "https://dx.doi.org/10.1371/journal.pone.0113768.s005", "https://dx.doi.org/10.1371/journal.pone.0113768.s006", "https://dx.doi.org/10.1371/journal.pone.0113768.s007", "https://dx.doi.org/10.1371/journal.pone.0113768.s008", "https://dx.doi.org/10.1371/journal.pone.0113768.s009", "https://dx.doi.org/10.1371/journal.pone.0113768.s010"], "stats"=>{"downloads"=>42, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcript_Profiling_Reveals_Auxin_and_Cytokinin_Signaling_Pathways_and_Transcription_Regulation_during_In_Vitro_Organogenesis_of_Ramie_Boehmeria_nivea_L_Gaud_/1249343", "title"=>"Transcript Profiling Reveals Auxin and Cytokinin Signaling Pathways and Transcription Regulation during <i>In Vitro</i> Organogenesis of Ramie (<i>Boehmeria nivea</i> L. Gaud)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-11-21 03:29:16"}

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Relative Metric

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