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...

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Vydáno v:	PloS one Ročník 2; číslo 11; s. e1235
Hlavní autoři:	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
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 28.11.2007 Public Library of Science (PLoS)
Témata:	Analysis Artificial chromosomes Bacteria Bioassays Biodiversity Biological activity Biological assays Biotechnology Chromosome Mapping Classification Cloning Complementary DNA Coverage Deoxyribonucleic acid DNA DNA microarrays DNA, Complementary - genetics DNA, Plant - genetics E coli Exons Gene expression Gene Expression Profiling Gene families Gene loci Gene mapping Gene sequencing Genes Genetics and Genomics/Plant Genetics and Gene Expression Genomes Genomics Incompatibility Introns Loci Mapping Nucleotide sequence Oryza - genetics Oryza sativa indica Oryza sativa japonica Plant Biology/Plant Genetics and Gene Expression Plant genetics Rice Structure-function relationships Transcription Transcription (Genetics) Transcription factors Japan
ISSN:	1932-6203, 1932-6203
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Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: YH PC JK S Kikuchi K Matsubara K Murakami. Performed the experiments: K Kamiya K Kurita MY AK TB NF KI YN SF MT NN HK TM K Satoh YO IC MN TH S Kanagawa TA JT MM DS HY. Analyzed the data: K Satoh TN K Suzuki KD. Contributed reagents/materials/analysis tools: K Satoh NK. Wrote the paper: K Satoh IC.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0001235