A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites
To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries we...
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| Veröffentlicht in: | The Plant cell 2002-03, Vol.14 (3), p.525-535 |
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| creator | Wu, Jianzhong Maehara, Tomoko Shimokawa, Takanori Yamamoto, Shinichi Harada, Chizuko Takazaki, Yuka Ono, Nozomi Mukai, Yoshiyuki Koike, Kazuhiro Yazaki, Jyunshi Fujii, Fumiko Shomura, Ayahiko Ando, Tsuyu Kono, Izumi Waki, Kazunori Yamamoto, Kimiko Yano, Masahiro Matsumoto, Takashi Sasaki, Takuji |
| description | To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only ∼21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals. |
| doi_str_mv | 10.1105/tpc.010274 |
| format | Article |
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Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only ∼21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.</description><identifier>ISSN: 1040-4651</identifier><identifier>EISSN: 1532-298X</identifier><identifier>DOI: 10.1105/tpc.010274</identifier><identifier>PMID: 11910001</identifier><language>eng</language><publisher>United States: American Society of Plant Biologists</publisher><subject>Chromosome Mapping - methods ; Chromosomes ; Chromosomes, Artificial, Yeast - genetics ; Cloning, Molecular ; Computational Biology ; Contig Mapping - methods ; DNA ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Genes ; Genetic mapping ; Genetic Markers ; Genetic resources ; Genetic screening ; Genome, Plant ; Genomes ; Genomics ; Genomics Articles ; Oryza - genetics ; Polymerase chain reaction ; Rice ; Tandem Repeat Sequences ; Transcription, Genetic - genetics ; Yeasts</subject><ispartof>The Plant cell, 2002-03, Vol.14 (3), p.525-535</ispartof><rights>Copyright 2002 American Society of Plant Biologists</rights><rights>Copyright American Society of Plant Physiologists Mar 2002</rights><rights>Copyright © 2002, American Society of Plant Biologists 2002</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c484t-4cf4ae45beee171ee993ec9067340ff373b8400e3f19fb865142aac6c1ed9f23</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/3871542$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/3871542$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,776,780,799,881,27903,27904,57995,58228</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11910001$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Jianzhong</creatorcontrib><creatorcontrib>Maehara, Tomoko</creatorcontrib><creatorcontrib>Shimokawa, Takanori</creatorcontrib><creatorcontrib>Yamamoto, Shinichi</creatorcontrib><creatorcontrib>Harada, Chizuko</creatorcontrib><creatorcontrib>Takazaki, Yuka</creatorcontrib><creatorcontrib>Ono, Nozomi</creatorcontrib><creatorcontrib>Mukai, Yoshiyuki</creatorcontrib><creatorcontrib>Koike, Kazuhiro</creatorcontrib><creatorcontrib>Yazaki, Jyunshi</creatorcontrib><creatorcontrib>Fujii, Fumiko</creatorcontrib><creatorcontrib>Shomura, Ayahiko</creatorcontrib><creatorcontrib>Ando, Tsuyu</creatorcontrib><creatorcontrib>Kono, Izumi</creatorcontrib><creatorcontrib>Waki, Kazunori</creatorcontrib><creatorcontrib>Yamamoto, Kimiko</creatorcontrib><creatorcontrib>Yano, Masahiro</creatorcontrib><creatorcontrib>Matsumoto, Takashi</creatorcontrib><creatorcontrib>Sasaki, Takuji</creatorcontrib><title>A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites</title><title>The Plant cell</title><addtitle>Plant Cell</addtitle><description>To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only ∼21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.</description><subject>Chromosome Mapping - methods</subject><subject>Chromosomes</subject><subject>Chromosomes, Artificial, Yeast - genetics</subject><subject>Cloning, Molecular</subject><subject>Computational Biology</subject><subject>Contig Mapping - methods</subject><subject>DNA</subject><subject>Expressed Sequence Tags</subject><subject>Gene Expression Profiling</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genetic mapping</subject><subject>Genetic Markers</subject><subject>Genetic resources</subject><subject>Genetic screening</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genomics Articles</subject><subject>Oryza - genetics</subject><subject>Polymerase chain reaction</subject><subject>Rice</subject><subject>Tandem Repeat Sequences</subject><subject>Transcription, Genetic - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The Plant cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Jianzhong</au><au>Maehara, Tomoko</au><au>Shimokawa, Takanori</au><au>Yamamoto, Shinichi</au><au>Harada, Chizuko</au><au>Takazaki, Yuka</au><au>Ono, Nozomi</au><au>Mukai, Yoshiyuki</au><au>Koike, Kazuhiro</au><au>Yazaki, Jyunshi</au><au>Fujii, Fumiko</au><au>Shomura, Ayahiko</au><au>Ando, Tsuyu</au><au>Kono, Izumi</au><au>Waki, Kazunori</au><au>Yamamoto, Kimiko</au><au>Yano, Masahiro</au><au>Matsumoto, Takashi</au><au>Sasaki, Takuji</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites</atitle><jtitle>The Plant cell</jtitle><addtitle>Plant Cell</addtitle><date>2002-03-01</date><risdate>2002</risdate><volume>14</volume><issue>3</issue><spage>525</spage><epage>535</epage><pages>525-535</pages><issn>1040-4651</issn><eissn>1532-298X</eissn><abstract>To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only ∼21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.</abstract><cop>United States</cop><pub>American Society of Plant Biologists</pub><pmid>11910001</pmid><doi>10.1105/tpc.010274</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Jstor Complete Legacy; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Chromosome Mapping - methods Chromosomes Chromosomes, Artificial, Yeast - genetics Cloning, Molecular Computational Biology Contig Mapping - methods DNA Expressed Sequence Tags Gene Expression Profiling Gene Library Genes Genetic mapping Genetic Markers Genetic resources Genetic screening Genome, Plant Genomes Genomics Genomics Articles Oryza - genetics Polymerase chain reaction Rice Tandem Repeat Sequences Transcription, Genetic - genetics Yeasts |
| title | A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites |
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