Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

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.

The RING Finger Ubiquitin E3 Ligase OsHTAS Enhances Heat Tolerance by Promoting H2O2-Induced Stomatal Closure in Rice

“…1A), which was verified by the full-length complementary DNA (cDNA) sequence (Kikuchi et al, 2003;Satoh et al, 2007;Kawahara et al, 2013). The deduced protein consisting of 414 amino acids was predicted to be a zinc finger family protein by a BLASTP search of the Michigan State University database (http://rice.plantbiology.msu.edu/).…”

Constitutive Expression of Rice MicroRNA528 Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass

“…The rice complementary DNA (cDNA) containing precursor miR528 (pre-miR528; AK073820; Knowledge-Based Oryza Molecular Biological Encyclopedia; http://cdna01.dna. affrc.go.jp/cDNA/; Kikuchi et al, 2003;Liu et al, 2005;Satoh et al, 2007) was amplified and then cloned into the binary vector pZH01, generating the Osa-miR528 overexpression gene construct, p35S-Osa-miR528/p35S-Hyg. As shown in Figure 2A, the Osa-miR528 gene was under the control of the CaMV 35S promoter and linked to the hygromycin resistance gene, Hyg, driven by the CaMV 35S promoter.…”

High-resolution mapping of open chromatin in the rice genome

“…Differentially expressed genes were also identified based on the Agilent microarray data (82,000 probes) with dyeswap (Satoh et al 2007). Fold change of gene expression (seedling/ callus) showed a moderate correlation between the two data sets (R = 0.64, PCC).…”

“…To accurately identify the genes differentially expressed in callus and seedling, we used the limma package of bioconductor (http://www. bioconductor.org/) to analyze the published microarray data in NCBI (Satoh et al 2007). We controlled the FDR of differentially expressed genes to under 0.05 for both microarray and RNA-seq data.…”