The R2R3-MYB Transcription Factor Gene Family in Maize
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{"title"=>"The R2R3-MYB Transcription Factor Gene Family in Maize", "type"=>"journal", "authors"=>[{"first_name"=>"Hai", "last_name"=>"Du"}, {"first_name"=>"Bo-Run", "last_name"=>"Feng"}, {"first_name"=>"Si-Si", "last_name"=>"Yang"}, {"first_name"=>"Yu-Bi", "last_name"=>"Huang"}, {"first_name"=>"Yi-Xiong", "last_name"=>"Tang"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0037463", "isbn"=>"10.1371/journal.pone.0037463", "pmid"=>"22719841"}, "id"=>"c8caa528-23e9-335a-baf0-c6af41b57291", "abstract"=>"MYB proteins comprise a large family of plant transcription factors, members of which perform a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). In the present study, we performed a comprehensive computational analysis, to yield a complete overview of the R2R3-MYB gene family in maize, including the phylogeny, expression patterns, and also its structural and functional characteristics. The MYB gene structure in maize and Arabidopsis were highly conserved, indicating that they were originally compact in size. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. The genome distribution strongly supports the hypothesis that segmental and tandem duplication contribute to the expansion of maize MYB genes. We also performed an updated and comprehensive classification of the R2R3-MYB gene families in maize and other plant species. The result revealed that the functions were conserved between maize MYB genes and their putative orthologs, demonstrating the origin and evolutionary diversification of plant MYB genes. Species-specific groups/subgroups may evolve or be lost during evolution, resulting in functional divergence. Expression profile study indicated that maize R2R3-MYB genes exhibit a variety of expression patterns, suggesting diverse functions. Furthermore, computational prediction potential targets of maize microRNAs (miRNAs) revealed that miR159, miR319, and miR160 may be implicated in regulating maize R2R3-MYB genes, suggesting roles of these miRNAs in post-transcriptional regulation and transcription networks. Our comparative analysis of R2R3-MYB genes in maize confirm and extend the sequence and functional characteristics of this gene family, and will facilitate future functional analysis of the MYB gene family in maize.", "link"=>"http://www.mendeley.com/research/r2r3myb-transcription-factor-gene-family-maize", "reader_count"=>115, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Researcher"=>23, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>11, "Lecturer"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Researcher"=>23, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>11, "Lecturer"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>93, "Chemical Engineering"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>93}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>6}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"South Korea"=>1, "United States"=>1, "Philippines"=>1, "Brazil"=>1, "United Kingdom"=>1, "Chile"=>1, "France"=>1, "Indonesia"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/626340"], "description"=>"<p>The shading of the alignment represents different degrees of conservation among sequences; the dark shading indicates identical residues, the light shading indicates conservative changes. The asterisks indicate conserved tryptophan residues (W) in the MYB domain. The positions of the three α-helices that form each MYB repeat are marked as Helix 1 to Helix 3. Residues involved in interaction are marked with dots; genes with these residues are underlined.</p>", "links"=>[], "tags"=>["amino", "alignment", "157", "maize", "r2r3-myb"], "article_id"=>296830, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ClustalW_amino_acid_sequence_alignment_of_157_typical_maize_R2R3_MYB_domains_/296830", "title"=>"ClustalW amino acid sequence alignment of 157 typical maize R2R3-MYB domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 01:53:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/324973", "https://ndownloader.figshare.com/files/325035", "https://ndownloader.figshare.com/files/325077", "https://ndownloader.figshare.com/files/325119", "https://ndownloader.figshare.com/files/325205", "https://ndownloader.figshare.com/files/325313", "https://ndownloader.figshare.com/files/325390", "https://ndownloader.figshare.com/files/325433", "https://ndownloader.figshare.com/files/325551"], "description"=>"<div><p>MYB proteins comprise a large family of plant transcription factors, members of which perform a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (<em>Zea mays</em>). In the present study, we performed a comprehensive computational analysis, to yield a complete overview of the R2R3-MYB gene family in maize, including the phylogeny, expression patterns, and also its structural and functional characteristics. The MYB gene structure in maize and <em>Arabidopsis</em> were highly conserved, indicating that they were originally compact in size. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. The genome distribution strongly supports the hypothesis that segmental and tandem duplication contribute to the expansion of maize MYB genes. We also performed an updated and comprehensive classification of the R2R3-MYB gene families in maize and other plant species. The result revealed that the functions were conserved between maize MYB genes and their putative orthologs, demonstrating the origin and evolutionary diversification of plant MYB genes. Species-specific groups/subgroups may evolve or be lost during evolution, resulting in functional divergence. Expression profile study indicated that maize R2R3-MYB genes exhibit a variety of expression patterns, suggesting diverse functions. Furthermore, computational prediction potential targets of maize microRNAs (miRNAs) revealed that miR159, miR319, and miR160 may be implicated in regulating maize R2R3-MYB genes, suggesting roles of these miRNAs in post-transcriptional regulation and transcription networks. Our comparative analysis of R2R3-MYB genes in maize confirm and extend the sequence and functional characteristics of this gene family, and will facilitate future functional analysis of the MYB gene family in maize.</p> </div>", "links"=>[], "tags"=>["r2r3-myb", "transcription", "maize"], "article_id"=>124135, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037463.s001", "https://dx.doi.org/10.1371/journal.pone.0037463.s002", "https://dx.doi.org/10.1371/journal.pone.0037463.s003", "https://dx.doi.org/10.1371/journal.pone.0037463.s004", "https://dx.doi.org/10.1371/journal.pone.0037463.s005", "https://dx.doi.org/10.1371/journal.pone.0037463.s006", "https://dx.doi.org/10.1371/journal.pone.0037463.s007", "https://dx.doi.org/10.1371/journal.pone.0037463.s008", "https://dx.doi.org/10.1371/journal.pone.0037463.s009"], "stats"=>{"downloads"=>35, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_R2R3_MYB_Transcription_Factor_Gene_Family_in_Maize/124135", "title"=>"The R2R3-MYB Transcription Factor Gene Family in Maize", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-07 01:08:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/626944"], "description"=>"<p>Black and gray shading indicate the presence of identical and conserved amino acid residues, respectively, in >75% of the aligned sequences. Consensus amino acid residues are shown below the alignment. The ‘‘x’’ indicates no conservation at this position.</p>", "links"=>[], "tags"=>["putative", "motif", "conserved", "g9"], "article_id"=>297431, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_putative_motif_conserved_in_group_G9_proteins_/297431", "title"=>"A putative motif conserved in group G9 proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 02:03:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/626874"], "description"=>"<p>The neighbor-joining tree includes 158 R2R3-MYB proteins from maize, 126 R2R3-MYB proteins from <i>Arabidopsis</i>, and a further 52 R2R3-MYB proteins from other plant species. The proteins are clustered into 37 subgroups (triangles), designated with a subgroup number (e.g., G1). Subfamilies are represented as collapsed triangles, with depth and width proportional to sequence divergence and size, respectively. The black triangles indicate that the subgroup includes ZmMYBs and AtMYBs; the hatched and white triangles indicate that the subgroup includes or excludes ZmMYBs, respectively. Bootstrap values <50% are not shown in the phylogenetic tree. Four proteins did not fit well into clusters. The first 25 subgroups were designated as previously reports of AtMYBs by Stracke et al. (2001) and Dubos et al. (2010). The subgroups were listed in round bracket with annotated functions, for reference. 12 new subgroups were added because of the increased data set.</p>", "links"=>[], "tags"=>["r2r3-myb", "proteins", "maize"], "article_id"=>297367, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g005", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_the_R2R3_MYB_proteins_from_maize_Zm_Arabidopsis_At_and_other_plant_species_/297367", "title"=>"Phylogenetic tree of the R2R3-MYB proteins from maize (Zm), <i>Arabidopsis</i> (At), and other plant species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 02:02:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/626697"], "description"=>"<p>Alignment of DNA-binding domains is representative of 12 intron patterns, named from a to l. Locations of introns are indicated by white triangles. The number within each triangle indicates the splicing phases of the MYB domain sequences: 0 refers to phase 0; 1 refers to phase 1; and 2 refers to phase 2. The number of ZmMYB proteins with each pattern is given on the right. The correlation of intron distribution patterns and phylogenetic subfamilies is provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037463#pone-0037463-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["intron", "patterns", "maize", "r2r3-myb", "dna-binding"], "article_id"=>297185, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_of_the_intron_distribution_patterns_within_the_maize_R2R3_MYB_DNA_binding_domains_/297185", "title"=>"Schematic of the intron distribution patterns within the maize R2R3-MYB DNA-binding domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 01:59:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/626561"], "description"=>"<p>A, The neighbor-joining (NJ) tree on the left includes 157 typical R2R3-MYB proteins from maize. The tree shows the 18 phylogenetic subgroups (S1–S18) marked with colored backgrounds, to facilitate subfamily identification with high predictive value. The numbers beside the branches represent bootstrap values (50%) based on 1000 replications. Eight proteins did not fit well into clusters. The colorful marker in the tree indicates the corresponding intron distribution patterns, as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037463#pone-0037463-g003\" target=\"_blank\">Figure 3</a>, below. B, The gene structure is presented by green exon (s), red MYB domain (s), blue UTR (s), and spaces between the colourful boxes corresponding to introns. The sizes of exons and introns can be estimated using the horizontal lines; the number indicated the phases of corresponding introns. C, The expression patterns of MYB genes in maize. The letter R above the column of expression data refers to root, ST refers to stem, L refers to leaf, FC refers to female catkins, MC refers to male catkins, and S refers to seed. D, Architecture of conserved protein motifs in 18 subfamilies. The motifs on the right were detected using MEME and are graphically represented as white boxes drawn to scale for a representative plant MYB protein of each subfamily.</p>", "links"=>[], "tags"=>["intron", "conserved", "subgroup", "designations", "r2r3-myb", "proteins", "maize"], "article_id"=>297047, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_intron_pattern_expression_pattern_architecture_of_conserved_protein_motifs_and_subgroup_designations_in_typical_R2R3_MYB_proteins_from_maize_Zm_/297047", "title"=>"Phylogenetic relationships, intron pattern, expression pattern, architecture of conserved protein motifs, and subgroup designations in typical R2R3-MYB proteins from maize (Zm).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 01:57:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/626787"], "description"=>"<p>The chromosomal position of each ZmMYB was mapped according to the maize genome. The chromosome number is indicated at the top of each chromosome. The number below indicates the number of ZmMYBs in each chromosome. The scale is in mega bases (Mb). The colored boxes indicate groups of predicted gene cluster with paralogous and syntenic genes on the chromosomes. The colored bars with numbers on the chromosomes indicate the 8 predicted duplication regions.</p>", "links"=>[], "tags"=>["maize", "r2r3-myb"], "article_id"=>297281, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Hai Du", "Bo-Run Feng", "Si-Si Yang", "Yu-Bi Huang", "Yi-Xiong Tang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037463.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosomal_locations_region_duplication_and_predicted_cluster_for_maize_R2R3_MYB_genes_/297281", "title"=>"Chromosomal locations, region duplication, and predicted cluster for maize R2R3-MYB genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-07 02:01:21"}

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Relative Metric

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