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Rice whole transcriptome surveyed by RNA-Seq and Paired-end technology

ABSTRACT: Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing

ORGANISM(S): Oryza sativa

PROVIDER: GSE16631 | GEO | 2010/03/01

SECONDARY ACCESSION(S): PRJNA117345

REPOSITORIES: GEO

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Project description:Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. This transcriptional complexity has been sampled mainly using hybridization-based methods under one or a few conditions. We applied direct high-throughput sequencing of cDNAs, complemented with different expression data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe, independently from available gene annotations. We interrogated transcriptomes under multiple conditions, including exponential proliferation, meiotic differentiation and environmental stress, and in RNA processing mutants, to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental, and genetic factors. High-throughput sequencing proved to be a powerful and quantitative method to deeply sample transcriptomes at unprecedented resolution. Unlike hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90% of the genome, including traces of RNAs that were not actively transcribed or rapidly degraded. The combined sequencing and strand-specific array data provided rich information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus refining the existing genome annotation. Sequence trans-reads spanning exon-exon or exon-intron junctions gave unique insight into a surprising variability in splicing efficiency across introns and genes. Splicing efficiency was largely coordinated with transcriptional efficiency, and hundreds of introns showed regulated splicing as a function of cellular proliferation or differentiation. ArrayExpress Release Date: 2008-12-03 Publication Title: Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution Publication Author List: Brian Wilhelm, Samuel Marguerat, Stephen Watt, Falk Schubert, Valerie Wood, Ian Goodhead, Christopher J. Penkett, Jane Rogers and Jurg Bahler Person Roles: submitter Person Last Name: Wilhelm Person First Name: Brian Person Mid Initials: Person Email: btw@sanger.ac.uk Person Phone: Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Bahler Person First Name: Jurg Person Mid Initials Person Email: jurg@sanger.ac.uk Person Phone Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Person Affiliation: Wellcome Trust Sanger Institute

Project description:Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array. keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray

Project description:Rice (Oryza sativa L.) is the main staple food for nearly half of the world’s population. Cereals, especially rice is deficient in micronutrients such as Fe. However, rice genotypes differ in grain Fe concentration (Panda B, et.al. Am J Plant Sci. 2014;5:2829-41. doi: 10.4236/ajps.2014.518299). The present study is focused on identification of gene(s) involved in Fe accumulation in developing rice grain through high throughput RNA-seq technology and to understand the basis of differential Fe accumulation in developing rice grain. Two cultivars of rice viz. Sharbati (high Fe) and Lalat (low Fe) differing in grain iron concentration were used in the study. Root and grain transcriptome sequences of these two cultivars (at mid-grain filling stage) were generated using RNA-Seq (Illumina Hiseq 2000 platform). For each genotype, on an average 9.7 and 7 Gb data was generated for grain and root samples, respectively. The short reads were aligned against the Nipponbare reference genome (IRGSP build 5.0), thereby successfully mapping 95% and 67% of the reads from grain and root samples, respectively. Genes known to be involved in Fe metabolism were analyzed for expression. Among the genes coding for phytosiderophore synthesizing enzymes, OsNAS1 and OsNAAT2 showed higher expression in the grains of Sharbati while OsDMAS1 had higher expression in its root. Of the 18 yellow-stripe like (YSL) genes in rice, only 11 were found to be expressed in the two cultivars. Out of these, 2 (OsYSL2 and OsYSL 8) were up-regulated in the grains of Sharbati highlighting their importance in the uptake of Fe from soil and its accumulation in the developing grain. Two other genes (OsFRO1 and OsIRT1) known to be involved in Fe uptake by the root were also found to be highly expressed in the root of Sharbati. Our findings suggest that higher grain iron concentration of cv. Sharbati might be due to higher expression of key Fe transporters (viz. OsYSL2, OsYSL8 and OsITR1) and root membrane bound OsFRO1, which give an advantage in terms of absorption, transport and assimilation of Fe by this cultivar as compared to the low iron containing cultivar, Lalat.

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Rice whole transcriptome surveyed by RNA-Seq and Paired-end technology

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