The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Cold Spring Harbor Laboratory
2006
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/166685 |
| _version_ | 1855513725361979392 |
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| author | Ammiraju, Jetty S.S. Luo, Meizhong Goicoechea, José L. Wang, Wenming Kudrna, Dave Mueller, Christopher Talag, Jayson Kim, HyeRan Sisneros, Nicholas B. Blackmon, Barbara Fang, Eric Tomkins, Jeffery B. Brar, Darshan Mackill, David McCouch, Susan Kurata, Nori Lambert, Georgina Galbraith, David W. Arumuganathan, K. Rao, Kiran Walling, Jason G. Gill, Navdeep Yu, Yeisoo SanMiguel, Phillip Soderlund, Carol Jackson, Scott Wing, Rod A. |
| author_browse | Ammiraju, Jetty S.S. Arumuganathan, K. Blackmon, Barbara Brar, Darshan Fang, Eric Galbraith, David W. Gill, Navdeep Goicoechea, José L. Jackson, Scott Kim, HyeRan Kudrna, Dave Kurata, Nori Lambert, Georgina Luo, Meizhong Mackill, David McCouch, Susan Mueller, Christopher Rao, Kiran SanMiguel, Phillip Sisneros, Nicholas B. Soderlund, Carol Talag, Jayson Tomkins, Jeffery B. Walling, Jason G. Wang, Wenming Wing, Rod A. Yu, Yeisoo |
| author_facet | Ammiraju, Jetty S.S. Luo, Meizhong Goicoechea, José L. Wang, Wenming Kudrna, Dave Mueller, Christopher Talag, Jayson Kim, HyeRan Sisneros, Nicholas B. Blackmon, Barbara Fang, Eric Tomkins, Jeffery B. Brar, Darshan Mackill, David McCouch, Susan Kurata, Nori Lambert, Georgina Galbraith, David W. Arumuganathan, K. Rao, Kiran Walling, Jason G. Gill, Navdeep Yu, Yeisoo SanMiguel, Phillip Soderlund, Carol Jackson, Scott Wing, Rod A. |
| author_sort | Ammiraju, Jetty S.S. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%–4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed. |
| format | Journal Article |
| id | CGSpace166685 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2006 |
| publishDateRange | 2006 |
| publishDateSort | 2006 |
| publisher | Cold Spring Harbor Laboratory |
| publisherStr | Cold Spring Harbor Laboratory |
| record_format | dspace |
| spelling | CGSpace1666852025-05-14T10:23:47Z The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza Ammiraju, Jetty S.S. Luo, Meizhong Goicoechea, José L. Wang, Wenming Kudrna, Dave Mueller, Christopher Talag, Jayson Kim, HyeRan Sisneros, Nicholas B. Blackmon, Barbara Fang, Eric Tomkins, Jeffery B. Brar, Darshan Mackill, David McCouch, Susan Kurata, Nori Lambert, Georgina Galbraith, David W. Arumuganathan, K. Rao, Kiran Walling, Jason G. Gill, Navdeep Yu, Yeisoo SanMiguel, Phillip Soderlund, Carol Jackson, Scott Wing, Rod A. bacterial artificial chromosomes genomes genome analysis nucleotide sequences retrotransposons wild relatives Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%–4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed. 2006-01 2024-12-19T12:56:33Z 2024-12-19T12:56:33Z Journal Article https://hdl.handle.net/10568/166685 en Cold Spring Harbor Laboratory Ammiraju, Jetty S.S.; Luo, Meizhong; Goicoechea, José L.; Wang, Wenming; Kudrna, Dave; Mueller, Christopher; Talag, Jayson; Kim, HyeRan; Sisneros, Nicholas B.; Blackmon, Barbara; Fang, Eric; Tomkins, Jeffery B.; Brar, Darshan; MacKill, David; McCouch, Susan; Kurata, Nori; Lambert, Georgina; Galbraith, David W.; Arumuganathan, K.; Rao, Kiran; Walling, Jason G.; Gill, Navdeep; Yu, Yeisoo; SanMiguel, Phillip; Soderlund, Carol; Jackson, Scott and Wing, Rod A. 2006. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res., Volume 16 no. 1 p. 140-147 |
| spellingShingle | bacterial artificial chromosomes genomes genome analysis nucleotide sequences retrotransposons wild relatives Ammiraju, Jetty S.S. Luo, Meizhong Goicoechea, José L. Wang, Wenming Kudrna, Dave Mueller, Christopher Talag, Jayson Kim, HyeRan Sisneros, Nicholas B. Blackmon, Barbara Fang, Eric Tomkins, Jeffery B. Brar, Darshan Mackill, David McCouch, Susan Kurata, Nori Lambert, Georgina Galbraith, David W. Arumuganathan, K. Rao, Kiran Walling, Jason G. Gill, Navdeep Yu, Yeisoo SanMiguel, Phillip Soderlund, Carol Jackson, Scott Wing, Rod A. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title | The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title_full | The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title_fullStr | The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title_full_unstemmed | The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title_short | The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza |
| title_sort | oryza bacterial artificial chromosome library resource construction and analysis of 12 deep coverage large insert bac libraries that represent the 10 genome types of the genus oryza |
| topic | bacterial artificial chromosomes genomes genome analysis nucleotide sequences retrotransposons wild relatives |
| url | https://hdl.handle.net/10568/166685 |
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