Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray

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dc.creatorSatoh, Kouji
dc.creatorDoi, Koji
dc.creatorNagata, Toshifumi
dc.creatorKishimoto, Naoki
dc.creatorSuzuki, Kohji
dc.creatorOtomo, Yasuhiro
dc.creatorKawai, Jun
dc.creatorNakamura, Mari
dc.creatorHirozane-Kishikawa, Tomoko
dc.creatorKanagawa, Saeko
dc.creatorArakawa, Takahiro
dc.creatorTakahashi-Iida, Juri
dc.creatorMurata, Mitsuyoshi
dc.creatorNinomiya, Noriko
dc.creatorSasaki, Daisuke
dc.creatorFukuda, Shiro
dc.creatorTagami, Michihira
dc.creatorYamagata, Harumi
dc.creatorKurita, Kanako
dc.creatorKamiya, Kozue
dc.creatorYamamoto, Mayu
dc.creatorKikuta, Ari
dc.creatorBito, Takahito
dc.creatorFujitsuka, Nahoko
dc.creatorIto, Kazue
dc.creatorKanamori, Hiroyuki
dc.creatorChoi, Il-Ryong
dc.creatorNagamura, Yoshiaki
dc.creatorMatsumoto, Takashi
dc.creatorMurakami, Kazuo
dc.creatorMatsubara, Ken-ichi
dc.creatorCarninci, Piero
dc.creatorHayashizaki, Yoshihide
dc.creatorKikuchi, Shoshi
dc.date2007-11-28
dc.date2024-12-19T12:56:13Z
dc.date2024-12-19T12:56:13Z
dc.date.accessioned2026-06-27T04:10:29Z
dc.descriptionRice (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.
dc.identifierhttps://hdl.handle.net/10568/166395
dc.identifier.urihttp://hdl.handle.net/123456789/23981
dc.languageen
dc.publisherPublic Library of Science
dc.rightsOpen Access
dc.sourceSatoh, 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
dc.subjectcomplementary dna
dc.subjectdna cloning
dc.subjectdna microarrays
dc.subjectgenes
dc.subjectgene expression
dc.subjectgenetic analysis
dc.subjectgenetic mapping
dc.titleGene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)