Whole Transcriptome Profiling of Maize during Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes
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{"title"=>"Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes", "type"=>"journal", "authors"=>[{"first_name"=>"Stella A.G.D.", "last_name"=>"Salvo", "scopus_author_id"=>"34870592700"}, {"first_name"=>"Candice N.", "last_name"=>"Hirsch", "scopus_author_id"=>"55621571300"}, {"first_name"=>"C. Robin", "last_name"=>"Buell", "scopus_author_id"=>"7003436847"}, {"first_name"=>"Shawn M.", "last_name"=>"Kaeppler", "scopus_author_id"=>"6701732823"}, {"first_name"=>"Heidi F.", "last_name"=>"Kaeppler", "scopus_author_id"=>"6701504475"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84908688766", "pui"=>"600319875", "doi"=>"10.1371/journal.pone.0111407", "pmid"=>"25356773", "scopus"=>"2-s2.0-84908688766", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)"}, "id"=>"5a1e1c55-8705-3a6e-ad6c-81133baf13b4", "abstract"=>"Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.", "link"=>"http://www.mendeley.com/research/whole-transcriptome-profiling-maize-during-early-somatic-embryogenesis-reveals-altered-expression-st", "reader_count"=>56, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>8, "Student > Bachelor"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>8, "Student > Bachelor"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Nursing and Health Professions"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>44, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>44}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2, "Sri Lanka"=>1, "Mexico"=>2, "Kenya"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1772717"], "description"=>"a<p>Fragments per kilobase of exon per million fragments mapped (FPKM) at 0, 24, 36, 48, and 72 h after placement on tissue culture initiation medium, genes with an 8-fold change in expression or greater as compared to the 0 h time point, and the assigned gene cluster designated by k-means analysis.</p><p>Expression of maize glutathione-S-transferase genes (ZmGST) and maize germin-like proteins (ZmGLP) in tissue culture.<sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111407#nt102\" target=\"_blank\">a</a></sup></p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223611, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.t003", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_maize_glutathione_S_transferase_genes_ZmGST_and_maize_germin_like_proteins_ZmGLP_in_tissue_culture_a_/1223611", "title"=>"Expression of maize glutathione-S-transferase genes (ZmGST) and maize germin-like proteins (ZmGLP) in tissue culture.<sup>a</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772711"], "description"=>"<p>Fragments per kilobase of exon model per million fragments mapped (FPKM) of maize genes associated with embryogenic callus induction expressed in immature zygotic embryos of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium where (A) is the maize ortholog to PINFORMED1 (ZmPIN1a), (B) is the maize ortholog to WUSCHEL (ZmWUS1), (C) is maize gene with high sequence similarity to CLAVATA (CLV1) and (D) is a maize ortholog to AGAMOUS (ZAG1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223605, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.g004", "stats"=>{"downloads"=>2, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_of_somatic_embryogenesis_genes_involved_in_callus_initiation_and_maintenance_/1223605", "title"=>"Gene expression of somatic embryogenesis genes involved in callus initiation and maintenance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772710"], "description"=>"<p>Average values of fragments per kilobase of exon model per million fragments mapped (FPKM) of genes involved in the induction of somatic embryogenesis expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium where (A), (B), and (C) are BBM-like maize genes with high sequence similarity to <i>Brassica napus</i> BABY BOOM (BnBBM1), (D) is maize LEAFY COTYLEDON1 (ZmLEC1), (E) is a maize gene with high sequence similarity to <i>Arabidopsis thaliana</i> LEAFY COTYLEDON2 (AtLEC2), and (F) is maize VIVIPARIOUS1 (VP1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223604, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.g003", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_of_somatic_embryogenesis_genes_involved_in_induction_/1223604", "title"=>"Gene expression of somatic embryogenesis genes involved in induction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772707"], "description"=>"<p>Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223601, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_changes_in_early_somatic_embryogenesis_/1223601", "title"=>"Gene expression changes in early somatic embryogenesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772720"], "description"=>"a<p>Fragments per kilobase of exon per million fragments mapped (FPKM) at 0, 24, 36, 48, and 72 h after placement on tissue culture initiation medium, genes with an 8-fold change in expression or greater as compared to the 0 h time point, and the assigned gene cluster designated by k-means analysis.</p><p>Expression of WUSCHEL-related maize WOX genes in tissue culture.<sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111407#nt103\" target=\"_blank\">a</a></sup></p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223613, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.t004", "stats"=>{"downloads"=>6, "page_views"=>56, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_WUSCHEL_related_maize_WOX_genes_in_tissue_culture_a_/1223613", "title"=>"Expression of WUSCHEL-related maize WOX genes in tissue culture.<sup>a</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772715"], "description"=>"<p>Somatic embryogenesis-related genes, National Center for Biotechnology Information (NCBI) accessions, and plant species where accession was previously characterized.</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223609, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.t002", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Somatic_embryogenesis_related_genes_National_Center_for_Biotechnology_Information_NCBI_accessions_and_plant_species_where_accession_was_previously_characterized_/1223609", "title"=>"Somatic embryogenesis-related genes, National Center for Biotechnology Information (NCBI) accessions, and plant species where accession was previously characterized.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772713"], "description"=>"<p>A proposed model of somatic embryogenesis-related gene expression networks as determined by coexpression (solid lines) with a correlation coefficient greater or equal to 0.9 between genes expressed during the early stages of somatic embryogenesis. Relative expression of transcripts detected in immature zygotic embryo explant tissues in tissue culture were detected in the inbred line A188 and reported as the average log2 expression displayed by color coded values as depicted by the figure legend for each gene. The first left most box under each gene name is the average log2 transformation of fragments per kilobase of exon model per million fragments mapped (FPKM) at 0 h, the second box at 24 h, the third at 36 h, the fourth at 48 h, and the fifth right most box is the average FPKM 72 h. Glutathione-S-transferases (GSTs) and germin-like proteins (GLPs) are stress response genes that are triggered in early somatic embryogenesis. BABY BOOM (BBM), an APETALA-like ethylene-responsive element transcription factor, and LEAFY COTYLEDON2 (LEC2), a B3 domain transcription factor, promote somatic embryogenesis. PINFORMED (PIN) genes mediate auxin transport and establish essential endogenous auxin concentrations in the cell. SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES (SERK) genes are also involved in somatic embryogenesis and hormone metabolism. WUSCHEL (WUS), a homeodomain transcription factor, regulates stem cell fate during embryo formation and development. AGAMOUS like-15 (AGL15), a MADS box transcription factor, also promotes somatic embryo formation and is also involved in meristem development. WUSCHEL-related homeobox domain (WOX) genes have also been detected during somatic embryogenesis in embryogenic genotypes but not in non-embryogenic genotypes.</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223607, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.g005", "stats"=>{"downloads"=>1, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_expression_of_coexpressed_somatic_embryogenesis_related_genes_/1223607", "title"=>"Relative expression of coexpressed somatic embryogenesis-related genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772714"], "description"=>"a<p>Fragments per kilobase of exon per million fragments mapped (FPKM) at 0, 24, 36, 48, and 72 h after placement on tissue culture initiation medium and the assigned gene cluster number determined by k-means analysis.</p><p>Highly expressed genes in immature zygotic embryo explants in tissue culture.<sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111407#nt101\" target=\"_blank\">a</a></sup></p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223608, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.t001", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Highly_expressed_genes_in_immature_zygotic_embryo_explants_in_tissue_culture_a_/1223608", "title"=>"Highly expressed genes in immature zygotic embryo explants in tissue culture.<sup>a</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772709"], "description"=>"<p>Log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in genes with greater than zero FPKM expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium grouped by expression trends as uncentered Pearson’s correlation coefficient in six k-means clusters.</p>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223603, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111407.g002", "stats"=>{"downloads"=>1, "page_views"=>47, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K_means_clustering_of_genes_expressed_during_early_somatic_embryogenesis_/1223603", "title"=>"K-means clustering of genes expressed during early somatic embryogenesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-30 03:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1772730", "https://ndownloader.figshare.com/files/1772731", "https://ndownloader.figshare.com/files/1772733", "https://ndownloader.figshare.com/files/1772734", "https://ndownloader.figshare.com/files/1772735", "https://ndownloader.figshare.com/files/1772736", "https://ndownloader.figshare.com/files/1772737", "https://ndownloader.figshare.com/files/1772738", "https://ndownloader.figshare.com/files/1772739", "https://ndownloader.figshare.com/files/1772740", "https://ndownloader.figshare.com/files/1772741", "https://ndownloader.figshare.com/files/1772742"], "description"=>"<div><p>Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.</p></div>", "links"=>[], "tags"=>["kinases", "sequence similarity", "stress response", "LEAFY COTYLEDON", "embryogenic cultures", "72 hours", "Hormone transport", "depth review", "plant species", "candidate genes", "tissue culture initiation medium", "genome transcriptome analysis", "gene expression", "agamous", "embryogenic callus formation", "maize embryogenic tissue culture initiation", "Altered Expression", "transcription factors BABY BOOM", "Maize genes", "PINFORMED", "Stress Factors", "embryo explants", "genomic factors", "Somatic Embryogenesis", "rna", "regenerable maize genotype", "embryogenic culture initiation", "Whole Transcriptome Profiling", "SOMATIC EMBRYOGENESIS RECEPTOR", "crop plants", "time course study", "clavata"], "article_id"=>1223617, "categories"=>["Biological Sciences"], "users"=>["Stella A. G. D. Salvo", "Candice N. Hirsch", "C. Robin Buell", "Shawn M. Kaeppler", "Heidi F. Kaeppler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0111407.s001", "https://dx.doi.org/10.1371/journal.pone.0111407.s002", "https://dx.doi.org/10.1371/journal.pone.0111407.s003", "https://dx.doi.org/10.1371/journal.pone.0111407.s004", "https://dx.doi.org/10.1371/journal.pone.0111407.s005", "https://dx.doi.org/10.1371/journal.pone.0111407.s006", "https://dx.doi.org/10.1371/journal.pone.0111407.s007", "https://dx.doi.org/10.1371/journal.pone.0111407.s008", "https://dx.doi.org/10.1371/journal.pone.0111407.s009", "https://dx.doi.org/10.1371/journal.pone.0111407.s010", "https://dx.doi.org/10.1371/journal.pone.0111407.s011", "https://dx.doi.org/10.1371/journal.pone.0111407.s012"], "stats"=>{"downloads"=>12, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_Transcriptome_Profiling_of_Maize_during_Early_Somatic_Embryogenesis_Reveals_Altered_Expression_of_Stress_Factors_and_Embryogenesis_Related_Genes_/1223617", "title"=>"Whole Transcriptome Profiling of Maize during Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-10-30 03:43:55"}

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Relative Metric

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