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Oryza sativa Japonica Group strain:Nipponbare

ABSTRACT: Comparison of spontaneous and somaclonal mutations of rice

PROVIDER: PRJDB5497 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR086972_1.fastq.gz	Fastqsanger.gz
	DRR086972_2.fastq.gz	Fastqsanger.gz
	DRR086973_1.fastq.gz	Fastqsanger.gz
	DRR086973_2.fastq.gz	Fastqsanger.gz
	DRR086974_1.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Oryza sativa Japonica Group

Project description:Analysis of somaclonal variation on the genome of regenerated rice

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Characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

Project description:Whole-genome DNA cytosine methylation profiling was used to characterize a knock-down RNA interference line of rice OsNRPD1

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Rice chromosome 10 alternate assembly

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Oryza sativa Japonica Group strain:Nipponbare

Project description:International Rice Genome Sequencing Project

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Oryza sativa Japonica Group

Project description:Whole genome sequence analysis of mutations in rice plants

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The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts.

Project description:BackgroundHigh-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome.ResultsA cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel.ConclusionThe data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Silicon response in rice siet4 mutant

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Study of intronic heterochromatin in the rice genome

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Mapping of rice endosperm starch altered gelatinization mutant

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