Structure and Architecture of the Maize Genome
Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of con...
Gespeichert in:
| Veröffentlicht in: | Plant physiology (Bethesda) 2005-12, Vol.139 (4), p.1612-1624 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 1624 |
|---|---|
| container_issue | 4 |
| container_start_page | 1612 |
| container_title | Plant physiology (Bethesda) |
| container_volume | 139 |
| creator | Haberer, Georg Young, Sarah Bharti, Arvind K Gundlach, Heidrun Raymond, Christina Fuks, Galina Butler, Ed Wing, Rod A Rounsley, Steve Birren, Bruce Nusbaum, Chad Mayer, Klaus F.X Messing, Joachim |
| description | Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes. |
| doi_str_mv | 10.1104/pp.105.068718 |
| format | Article |
| fullrecord | <record><control><sourceid>jstor_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_68884360</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><jstor_id>4281990</jstor_id><sourcerecordid>4281990</sourcerecordid><originalsourceid>FETCH-LOGICAL-c473t-8cedf4a3eafa44aba66ad88267c11055a36dc1ad28b7e8403119c262eb7b8dca3</originalsourceid><addsrcrecordid>eNqFkb1PwzAQxS0EoqUwsiHIAluCv2I7Y1VBQSpiKJ2ji-PQVEkT7GSAvx6XRDAy3dPdT09P7xC6JDgiBPP7to0IjiMslCTqCE1JzGhIY66O0RRjr7FSyQSdObfDGBNG-CmaEMFYorCcomjd2V53vTUB7PNgbvW27MywaIqg25rgBcovEyzNvqnNOTopoHLmYpwztHl8eFs8havX5fNivgo1l6wLlTZ5wYEZKIBzyEAIyJWiQmofOo6BiVwTyKnKpFEcM0ISTQU1mcxUroHN0N3g29rmozeuS-vSaVNVsDdN71KhlOJM4H9BIjnl_AcMB1DbxjlrirS1ZQ32MyU4PTSZtq2XcTo06fnr0bjPapP_0WN1HrgdAXAaqsLCXpfuj5MsZiQRnrsauJ3rGvt751SRJDnkuhnOBTQpvFtvsVlT_yjsM_HYm3wDe4OMqg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>17424460</pqid></control><display><type>article</type><title>Structure and Architecture of the Maize Genome</title><source>MEDLINE</source><source>JSTOR Archive Collection A-Z Listing</source><source>Oxford University Press Journals All Titles (1996-Current)</source><source>EZB-FREE-00999 freely available EZB journals</source><creator>Haberer, Georg ; Young, Sarah ; Bharti, Arvind K ; Gundlach, Heidrun ; Raymond, Christina ; Fuks, Galina ; Butler, Ed ; Wing, Rod A ; Rounsley, Steve ; Birren, Bruce ; Nusbaum, Chad ; Mayer, Klaus F.X ; Messing, Joachim</creator><creatorcontrib>Haberer, Georg ; Young, Sarah ; Bharti, Arvind K ; Gundlach, Heidrun ; Raymond, Christina ; Fuks, Galina ; Butler, Ed ; Wing, Rod A ; Rounsley, Steve ; Birren, Bruce ; Nusbaum, Chad ; Mayer, Klaus F.X ; Messing, Joachim</creatorcontrib><description>Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.</description><identifier>ISSN: 0032-0889</identifier><identifier>EISSN: 1532-2548</identifier><identifier>DOI: 10.1104/pp.105.068718</identifier><identifier>PMID: 16339807</identifier><identifier>CODEN: PPHYA5</identifier><language>eng</language><publisher>Rockville, MD: American Society of Plant Biologists</publisher><subject>Arabidopsis thaliana ; bacterial artificial chromosomes ; Base Composition ; Bioinformatics ; Biological and medical sciences ; Chromosomes, Artificial, Bacterial - genetics ; Codon - genetics ; Corn ; Datasets ; DNA ; DNA, Plant - chemistry ; DNA, Plant - genetics ; Exons ; expressed sequence tags ; Fundamental and applied biological sciences. Psychology ; Gene Expression ; Gene Library ; Genes ; Genes, Plant ; Genes. Genome ; genome ; Genome, Plant ; Genomes ; Genomics ; Introns ; Molecular and cellular biology ; Molecular genetics ; Multigene Family ; Oryza sativa ; plant genetics ; Repetitive Sequences, Nucleic Acid ; Rice ; sequence analysis ; Sequencing ; Zea mays ; Zea mays - genetics</subject><ispartof>Plant physiology (Bethesda), 2005-12, Vol.139 (4), p.1612-1624</ispartof><rights>Copyright 2005 American Society of Plant Biologists</rights><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c473t-8cedf4a3eafa44aba66ad88267c11055a36dc1ad28b7e8403119c262eb7b8dca3</citedby><cites>FETCH-LOGICAL-c473t-8cedf4a3eafa44aba66ad88267c11055a36dc1ad28b7e8403119c262eb7b8dca3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/4281990$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/4281990$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,27924,27925,58017,58250</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17353196$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16339807$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Haberer, Georg</creatorcontrib><creatorcontrib>Young, Sarah</creatorcontrib><creatorcontrib>Bharti, Arvind K</creatorcontrib><creatorcontrib>Gundlach, Heidrun</creatorcontrib><creatorcontrib>Raymond, Christina</creatorcontrib><creatorcontrib>Fuks, Galina</creatorcontrib><creatorcontrib>Butler, Ed</creatorcontrib><creatorcontrib>Wing, Rod A</creatorcontrib><creatorcontrib>Rounsley, Steve</creatorcontrib><creatorcontrib>Birren, Bruce</creatorcontrib><creatorcontrib>Nusbaum, Chad</creatorcontrib><creatorcontrib>Mayer, Klaus F.X</creatorcontrib><creatorcontrib>Messing, Joachim</creatorcontrib><title>Structure and Architecture of the Maize Genome</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.</description><subject>Arabidopsis thaliana</subject><subject>bacterial artificial chromosomes</subject><subject>Base Composition</subject><subject>Bioinformatics</subject><subject>Biological and medical sciences</subject><subject>Chromosomes, Artificial, Bacterial - genetics</subject><subject>Codon - genetics</subject><subject>Corn</subject><subject>Datasets</subject><subject>DNA</subject><subject>DNA, Plant - chemistry</subject><subject>DNA, Plant - genetics</subject><subject>Exons</subject><subject>expressed sequence tags</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genes. Genome</subject><subject>genome</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Introns</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Multigene Family</subject><subject>Oryza sativa</subject><subject>plant genetics</subject><subject>Repetitive Sequences, Nucleic Acid</subject><subject>Rice</subject><subject>sequence analysis</subject><subject>Sequencing</subject><subject>Zea mays</subject><subject>Zea mays - genetics</subject><issn>0032-0889</issn><issn>1532-2548</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkb1PwzAQxS0EoqUwsiHIAluCv2I7Y1VBQSpiKJ2ji-PQVEkT7GSAvx6XRDAy3dPdT09P7xC6JDgiBPP7to0IjiMslCTqCE1JzGhIY66O0RRjr7FSyQSdObfDGBNG-CmaEMFYorCcomjd2V53vTUB7PNgbvW27MywaIqg25rgBcovEyzNvqnNOTopoHLmYpwztHl8eFs8havX5fNivgo1l6wLlTZ5wYEZKIBzyEAIyJWiQmofOo6BiVwTyKnKpFEcM0ISTQU1mcxUroHN0N3g29rmozeuS-vSaVNVsDdN71KhlOJM4H9BIjnl_AcMB1DbxjlrirS1ZQ32MyU4PTSZtq2XcTo06fnr0bjPapP_0WN1HrgdAXAaqsLCXpfuj5MsZiQRnrsauJ3rGvt751SRJDnkuhnOBTQpvFtvsVlT_yjsM_HYm3wDe4OMqg</recordid><startdate>20051201</startdate><enddate>20051201</enddate><creator>Haberer, Georg</creator><creator>Young, Sarah</creator><creator>Bharti, Arvind K</creator><creator>Gundlach, Heidrun</creator><creator>Raymond, Christina</creator><creator>Fuks, Galina</creator><creator>Butler, Ed</creator><creator>Wing, Rod A</creator><creator>Rounsley, Steve</creator><creator>Birren, Bruce</creator><creator>Nusbaum, Chad</creator><creator>Mayer, Klaus F.X</creator><creator>Messing, Joachim</creator><general>American Society of Plant Biologists</general><general>American Society of Plant Physiologists</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20051201</creationdate><title>Structure and Architecture of the Maize Genome</title><author>Haberer, Georg ; Young, Sarah ; Bharti, Arvind K ; Gundlach, Heidrun ; Raymond, Christina ; Fuks, Galina ; Butler, Ed ; Wing, Rod A ; Rounsley, Steve ; Birren, Bruce ; Nusbaum, Chad ; Mayer, Klaus F.X ; Messing, Joachim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c473t-8cedf4a3eafa44aba66ad88267c11055a36dc1ad28b7e8403119c262eb7b8dca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Arabidopsis thaliana</topic><topic>bacterial artificial chromosomes</topic><topic>Base Composition</topic><topic>Bioinformatics</topic><topic>Biological and medical sciences</topic><topic>Chromosomes, Artificial, Bacterial - genetics</topic><topic>Codon - genetics</topic><topic>Corn</topic><topic>Datasets</topic><topic>DNA</topic><topic>DNA, Plant - chemistry</topic><topic>DNA, Plant - genetics</topic><topic>Exons</topic><topic>expressed sequence tags</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression</topic><topic>Gene Library</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genes. Genome</topic><topic>genome</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Introns</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Multigene Family</topic><topic>Oryza sativa</topic><topic>plant genetics</topic><topic>Repetitive Sequences, Nucleic Acid</topic><topic>Rice</topic><topic>sequence analysis</topic><topic>Sequencing</topic><topic>Zea mays</topic><topic>Zea mays - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Haberer, Georg</creatorcontrib><creatorcontrib>Young, Sarah</creatorcontrib><creatorcontrib>Bharti, Arvind K</creatorcontrib><creatorcontrib>Gundlach, Heidrun</creatorcontrib><creatorcontrib>Raymond, Christina</creatorcontrib><creatorcontrib>Fuks, Galina</creatorcontrib><creatorcontrib>Butler, Ed</creatorcontrib><creatorcontrib>Wing, Rod A</creatorcontrib><creatorcontrib>Rounsley, Steve</creatorcontrib><creatorcontrib>Birren, Bruce</creatorcontrib><creatorcontrib>Nusbaum, Chad</creatorcontrib><creatorcontrib>Mayer, Klaus F.X</creatorcontrib><creatorcontrib>Messing, Joachim</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Plant physiology (Bethesda)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Haberer, Georg</au><au>Young, Sarah</au><au>Bharti, Arvind K</au><au>Gundlach, Heidrun</au><au>Raymond, Christina</au><au>Fuks, Galina</au><au>Butler, Ed</au><au>Wing, Rod A</au><au>Rounsley, Steve</au><au>Birren, Bruce</au><au>Nusbaum, Chad</au><au>Mayer, Klaus F.X</au><au>Messing, Joachim</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure and Architecture of the Maize Genome</atitle><jtitle>Plant physiology (Bethesda)</jtitle><addtitle>Plant Physiol</addtitle><date>2005-12-01</date><risdate>2005</risdate><volume>139</volume><issue>4</issue><spage>1612</spage><epage>1624</epage><pages>1612-1624</pages><issn>0032-0889</issn><eissn>1532-2548</eissn><coden>PPHYA5</coden><abstract>Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.</abstract><cop>Rockville, MD</cop><pub>American Society of Plant Biologists</pub><pmid>16339807</pmid><doi>10.1104/pp.105.068718</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0032-0889 |
| ispartof | Plant physiology (Bethesda), 2005-12, Vol.139 (4), p.1612-1624 |
| issn | 0032-0889 1532-2548 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_68884360 |
| source | MEDLINE; JSTOR Archive Collection A-Z Listing; Oxford University Press Journals All Titles (1996-Current); EZB-FREE-00999 freely available EZB journals |
| subjects | Arabidopsis thaliana bacterial artificial chromosomes Base Composition Bioinformatics Biological and medical sciences Chromosomes, Artificial, Bacterial - genetics Codon - genetics Corn Datasets DNA DNA, Plant - chemistry DNA, Plant - genetics Exons expressed sequence tags Fundamental and applied biological sciences. Psychology Gene Expression Gene Library Genes Genes, Plant Genes. Genome genome Genome, Plant Genomes Genomics Introns Molecular and cellular biology Molecular genetics Multigene Family Oryza sativa plant genetics Repetitive Sequences, Nucleic Acid Rice sequence analysis Sequencing Zea mays Zea mays - genetics |
| title | Structure and Architecture of the Maize Genome |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-02T20%3A10%3A33IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-jstor_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Structure%20and%20Architecture%20of%20the%20Maize%20Genome&rft.jtitle=Plant%20physiology%20(Bethesda)&rft.au=Haberer,%20Georg&rft.date=2005-12-01&rft.volume=139&rft.issue=4&rft.spage=1612&rft.epage=1624&rft.pages=1612-1624&rft.issn=0032-0889&rft.eissn=1532-2548&rft.coden=PPHYA5&rft_id=info:doi/10.1104/pp.105.068718&rft_dat=%3Cjstor_proqu%3E4281990%3C/jstor_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=17424460&rft_id=info:pmid/16339807&rft_jstor_id=4281990&rfr_iscdi=true |