ArticlePloS one2007
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 58 citations in OpenAlex.
- Melatonin-Regulated Chaperone Binding Protein Plays a Key Role in Cadmium Stress Tolerance in Rice, Revealed by the Functional Characterization of a Novel SerotoninInternational journal of molecular sciences · 2024Article
- Comparative analysis of the transcriptomes of two rice subspecies during domestication.Scientific reports · 2021Article
- The RING Finger Ubiquitin E3 Ligase OsHTAS Enhances Heat Tolerance by Promoting H2O2-Induced Stomatal Closure in Rice.Plant physiology · 2016Article
- Constitutive Expression of Rice MicroRNA528 Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass.Plant physiology · 2015Article
- Application of resequencing to rice genomics, functional genomics and evolutionary analysis.Rice (New York, N.Y.) · 2014Review
- Comparative analysis of microRNA promoters in Arabidopsis and rice.Genomics, proteomics & bioinformatics · 2013Article
- Engineering the Oryza sativa cell wall with rice NAC transcription factors regulating secondary wall formation.Frontiers in plant science · 2013Article
- Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints.BMC genomics · 2012Article
- Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis.BMC genomics · 2012Article
- High-resolution mapping of open chromatin in the rice genome.Genome research · 2012Article
- Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice.Molecular genetics and genomics : MGG · 2010Article
- Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome research · 2010Article
- Article
- Characterization of the rice PHO1 gene family reveals a key role for OsPHO1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons.Plant physiology · 2010Article
- Evidence-based gene predictions in plant genomes.Genome research · 2009Article
- Article
- High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources.DNA research : an international journal for rapid publication of reports on genes and genomes · 2009Article
- Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis.Plant physiology · 2009Article
- Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943.DNA research : an international journal for rapid publication of reports on genes and genomes · 2008Article
Corrections and comments
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Authors and funding
34 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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