Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray
Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Public Library of Science
2007
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/166395 |
| _version_ | 1855524137582198784 |
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| author | Satoh, Kouji Doi, Koji Nagata, Toshifumi Kishimoto, Naoki Suzuki, Kohji Otomo, Yasuhiro Kawai, Jun Nakamura, Mari Hirozane-Kishikawa, Tomoko Kanagawa, Saeko Arakawa, Takahiro Takahashi-Iida, Juri Murata, Mitsuyoshi Ninomiya, Noriko Sasaki, Daisuke Fukuda, Shiro Tagami, Michihira Yamagata, Harumi Kurita, Kanako Kamiya, Kozue Yamamoto, Mayu Kikuta, Ari Bito, Takahito Fujitsuka, Nahoko Ito, Kazue Kanamori, Hiroyuki Choi, Il-Ryong Nagamura, Yoshiaki Matsumoto, Takashi Murakami, Kazuo Matsubara, Ken-ichi Carninci, Piero Hayashizaki, Yoshihide Kikuchi, Shoshi |
| author_browse | Arakawa, Takahiro Bito, Takahito Carninci, Piero Choi, Il-Ryong Doi, Koji Fujitsuka, Nahoko Fukuda, Shiro Hayashizaki, Yoshihide Hirozane-Kishikawa, Tomoko Ito, Kazue Kamiya, Kozue Kanagawa, Saeko Kanamori, Hiroyuki Kawai, Jun Kikuchi, Shoshi Kikuta, Ari Kishimoto, Naoki Kurita, Kanako Matsubara, Ken-ichi Matsumoto, Takashi Murakami, Kazuo Murata, Mitsuyoshi Nagamura, Yoshiaki Nagata, Toshifumi Nakamura, Mari Ninomiya, Noriko Otomo, Yasuhiro Sasaki, Daisuke Satoh, Kouji Suzuki, Kohji Tagami, Michihira Takahashi-Iida, Juri Yamagata, Harumi Yamamoto, Mayu |
| author_facet | Satoh, Kouji Doi, Koji Nagata, Toshifumi Kishimoto, Naoki Suzuki, Kohji Otomo, Yasuhiro Kawai, Jun Nakamura, Mari Hirozane-Kishikawa, Tomoko Kanagawa, Saeko Arakawa, Takahiro Takahashi-Iida, Juri Murata, Mitsuyoshi Ninomiya, Noriko Sasaki, Daisuke Fukuda, Shiro Tagami, Michihira Yamagata, Harumi Kurita, Kanako Kamiya, Kozue Yamamoto, Mayu Kikuta, Ari Bito, Takahito Fujitsuka, Nahoko Ito, Kazue Kanamori, Hiroyuki Choi, Il-Ryong Nagamura, Yoshiaki Matsumoto, Takashi Murakami, Kazuo Matsubara, Ken-ichi Carninci, Piero Hayashizaki, Yoshihide Kikuchi, Shoshi |
| author_sort | Satoh, Kouji |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria. |
| format | Journal Article |
| id | CGSpace166395 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2007 |
| publishDateRange | 2007 |
| publishDateSort | 2007 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1663952025-01-24T14:12:48Z Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray Satoh, Kouji Doi, Koji Nagata, Toshifumi Kishimoto, Naoki Suzuki, Kohji Otomo, Yasuhiro Kawai, Jun Nakamura, Mari Hirozane-Kishikawa, Tomoko Kanagawa, Saeko Arakawa, Takahiro Takahashi-Iida, Juri Murata, Mitsuyoshi Ninomiya, Noriko Sasaki, Daisuke Fukuda, Shiro Tagami, Michihira Yamagata, Harumi Kurita, Kanako Kamiya, Kozue Yamamoto, Mayu Kikuta, Ari Bito, Takahito Fujitsuka, Nahoko Ito, Kazue Kanamori, Hiroyuki Choi, Il-Ryong Nagamura, Yoshiaki Matsumoto, Takashi Murakami, Kazuo Matsubara, Ken-ichi Carninci, Piero Hayashizaki, Yoshihide Kikuchi, Shoshi complementary dna dna cloning dna microarrays genes gene expression genetic analysis genetic mapping Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria. 2007-11-28 2024-12-19T12:56:13Z 2024-12-19T12:56:13Z Journal Article https://hdl.handle.net/10568/166395 en Open Access Public Library of Science Satoh, Kouji; Doi, Koji; Nagata, Toshifumi; Kishimoto, Naoki; Suzuki, Kohji; Otomo, Yasuhiro; Kawai, Jun; Nakamura, Mari; Hirozane-Kishikawa, Tomoko; Kanagawa, Saeko; Arakawa, Takahiro; Takahashi-Iida, Juri; Murata, Mitsuyoshi; Ninomiya, Noriko; Sasaki, Daisuke; Fukuda, Shiro; Tagami, Michihira; Yamagata, Harumi; Kurita, Kanako; Kamiya, Kozue; Yamamoto, Mayu; Kikuta, Ari; Bito, Takahito; Fujitsuka, Nahoko; Ito, Kazue; Kanamori, Hiroyuki; Choi, Il-Ryong; Nagamura, Yoshiaki; Matsumoto, Takashi; Murakami, Kazuo; Matsubara, Ken-ichi; Carninci, Piero; Hayashizaki, Yoshihide and Kikuchi, Shoshi. 2007. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE, Volume 2 no. 11 p. e1235 |
| spellingShingle | complementary dna dna cloning dna microarrays genes gene expression genetic analysis genetic mapping Satoh, Kouji Doi, Koji Nagata, Toshifumi Kishimoto, Naoki Suzuki, Kohji Otomo, Yasuhiro Kawai, Jun Nakamura, Mari Hirozane-Kishikawa, Tomoko Kanagawa, Saeko Arakawa, Takahiro Takahashi-Iida, Juri Murata, Mitsuyoshi Ninomiya, Noriko Sasaki, Daisuke Fukuda, Shiro Tagami, Michihira Yamagata, Harumi Kurita, Kanako Kamiya, Kozue Yamamoto, Mayu Kikuta, Ari Bito, Takahito Fujitsuka, Nahoko Ito, Kazue Kanamori, Hiroyuki Choi, Il-Ryong Nagamura, Yoshiaki Matsumoto, Takashi Murakami, Kazuo Matsubara, Ken-ichi Carninci, Piero Hayashizaki, Yoshihide Kikuchi, Shoshi Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title | Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title_full | Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title_fullStr | Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title_full_unstemmed | Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title_short | Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray |
| title_sort | gene organization in rice revealed by full length cdna mapping and gene expression analysis through microarray |
| topic | complementary dna dna cloning dna microarrays genes gene expression genetic analysis genetic mapping |
| url | https://hdl.handle.net/10568/166395 |
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