Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize
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{"title"=>"Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize", "type"=>"journal", "authors"=>[{"first_name"=>"James C.", "last_name"=>"Schnable", "scopus_author_id"=>"36098331900"}, {"first_name"=>"Michael", "last_name"=>"Freeling", "scopus_author_id"=>"7005942891"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361419325", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0017855", "scopus"=>"2-s2.0-79952495788", "pmid"=>"21423772", "sgr"=>"79952495788"}, "id"=>"8ca04765-cfce-389f-a04a-7e945f6f8f61", "abstract"=>"Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these \"classical\" maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5-12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of \"grasses as a single genetic system,\" where what is learned in one grass may be applied to another.", "link"=>"http://www.mendeley.com/research/genes-identified-visible-mutant-phenotypes-show-increased-bias-toward-one-two-subgenomes-maize", "reader_count"=>77, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>9, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>9, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>69, "Psychology"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>69}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>4, "China"=>2, "Mexico"=>1, "Nigeria"=>1, "Germany"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/792077"], "description"=>"<p>Branch lengths not to scale. *The genome sequencing of foxtail millet by\n the joint genome institute is complete, but has not yet been published.\n Therefore it is not included in our analyses (SI 1). **Projects to\n sequence the genomes of barley and wheat are announced or in progress.</p>", "links"=>[], "tags"=>["relationships", "notable", "sequenced", "grass"], "article_id"=>462448, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["James C. Schnable", "Michael Freeling"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017855.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_notable_and_sequenced_grass____species_/462448", "title"=>"Phylogenetic relationships of notable and sequenced grass\n species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-10 00:40:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/396284", "https://ndownloader.figshare.com/files/396311", "https://ndownloader.figshare.com/files/396330"], "description"=>"<div><p>Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (<em>Zea mays</em> L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these “classical” maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5–12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of “grasses as a single genetic system,” where what is learned in one grass may be applied to another.</p> </div>", "links"=>[], "tags"=>["genes", "identified", "mutant", "phenotypes", "bias", "subgenomes", "maize"], "article_id"=>138283, "categories"=>["Genetics", "Cell Biology", "Evolutionary Biology"], "users"=>["James C. Schnable", "Michael Freeling"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017855.s001", "https://dx.doi.org/10.1371/journal.pone.0017855.s002", "https://dx.doi.org/10.1371/journal.pone.0017855.s003"], "stats"=>{"downloads"=>8, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genes_Identified_by_Visible_Mutant_Phenotypes_Show_Increased_Bias___toward_One_of_Two_Subgenomes_of_Maize/138283", "title"=>"Genes Identified by Visible Mutant Phenotypes Show Increased Bias\n toward One of Two Subgenomes of Maize", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-10 02:18:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/792304"], "description"=>"<p>Comparison of the distribution of genes retained syntenically in at least\n one other grass species between the two subgenomes of maize as well as\n whether genes possess retained homeologs from the maize whole genome\n duplication. For syntenically retained maize genes with full length cDNA\n support N = 17956. For the subset of the classical\n maize gene list that are syntenically retained\n N = 429. For the subset of genes that were first\n identified by mutant phenotype and are syntenically retained\n N = 102.</p>", "links"=>[], "tags"=>["maize", "genes", "maize"], "article_id"=>462676, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["James C. Schnable", "Michael Freeling"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017855.g004", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_classical_maize_genes_between_the_two_maize____subgenomes_/462676", "title"=>"Distribution of classical maize genes between the two maize\n subgenomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-10 00:44:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/792224"], "description"=>"<p>Comparison of the proportion of genes identified by a mutant phenotype\n prior to cloning (N = 111), all classical maize\n genes (N = 464), and all maize genes supported by\n full length cDNA evidence (N = 34579) for which\n syntenic orthologs could be identified in the other three grass species\n with sequenced genomes: sorghum, rice, and brachypodium.</p>", "links"=>[], "tags"=>["maize", "genes", "other"], "article_id"=>462599, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["James C. Schnable", "Michael Freeling"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017855.g003", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Syntenic_conservation_of_the_classical_maize_genes_in_other____grasses_/462599", "title"=>"Syntenic conservation of the classical maize genes in other\n grasses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-10 00:43:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/792141"], "description"=>"<p>Graphics from GEvo comparative sequence alignment tool. Annotated cDNAs\n from GenBank are compared to regions of the maize B73_refgen2 genome.\n Features on the forward strand are displayed above the dotted line, and\n features on the reserve strand are displayed below the line. Grey lines\n mark the extent of gene models with CDS sequences in green and UTR\n sequences in blue. Orange bars mark the gaps between assembled contigs\n of the maize genome (stretches of N's). Red boxes connected by\n lines show sequences identified as homologous by blastn. A. A comparison\n of the coding sequence of <i>aspartate kinase-homoserine\n dehydrogenase1</i> to the region of maize chromosome 4 that\n contains the three gene models –from left to right, GRMZM2G365423,\n GRMZM2G389303, and GRMZM2G437977 -- among which the exons of this gene\n have been divided. An interactive version of this graphic can be\n regenerated in GEvo using the following link: <a href=\"http://genomevolution.org/r/25xh\" target=\"_blank\">http://genomevolution.org/r/25xh</a> B. A comparison of\n <i>cytokinin oxidase1</i> to GRMZM2G146644, a gene model\n which includes the 5' and 3' ends of <i>cko1</i> but\n has also incorporated unrelated exons from another maize genome contig.\n Regenerate analysis: <a href=\"http://genomevolution.org/r/25s5\" target=\"_blank\">http://genomevolution.org/r/25s5</a> C. The coding sequence\n of ferredoxin homeolog2 which maps to a region of the maize genome\n annotated as the 3' UTR of GRMZM2G147266. Regenerate analysis:\n <a href=\"http://genomevolution.org/r/25s7\" target=\"_blank\">http://genomevolution.org/r/25s7</a>.</p>", "links"=>[], "tags"=>["manually", "errors", "maize", "gene"], "article_id"=>462511, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["James C. Schnable", "Michael Freeling"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017855.g002", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_manually_identified_errors_in_maize_gene____annotations_/462511", "title"=>"Examples of manually identified errors in maize gene\n annotations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-10 00:41:51"}

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Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[308, 573, 694, 810, 910, 993, 1084, 1153, 1231, 1302, 1368, 1447, 1509, 1581, 1659, 1737, 1803, 1867, 1937, 2011, 2067, 2142, 2196, 2260, 2318, 2376, 2413, 2492, 2584, 2650, 2729, 2803, 2868, 2929, 3006, 3082, 3146]}]}
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