Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
Lu, Tingting; Lu, Guojun; Fan, Danlin; Zhu, Chuanrang; Li, Wei; Zhao, Qiang; Feng, Qi; Zhao, Yan; Guo, Yunli; Li, Wenjun; Huang, Xuehui; Han, Bin
2010
Source PublicationGENOME RESEARCH
ISSN1088-9051
EISSN1549-5469
Volume20Issue:9Pages:1238-1249
Status已发表
DOI10.1101/gr.106120.110
Abstract

The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Otyza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (<20%). We found that similar to 48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 5' and/or 3' ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.

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Indexed BySCI
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000281520400009
PublisherCOLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
WOS KeywordGENE-EXPRESSION ; DRAFT SEQUENCE ; GENOME ; ARABIDOPSIS ; MICROARRAY ; JAPONICA ; REVEALS ; INDICA ; COLLECTION ; GENERATION
Original Document TypeArticle
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Cited Times:233[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttps://kms.shanghaitech.edu.cn/handle/2MSLDSTB/119660
Collection个人在本单位外知识产出
Corresponding AuthorHan, Bin
Affiliation1.Chinese Acad Sci, Natl Ctr Gene Res, Shanghai 200233, Peoples R China
2.Chinese Acad Sci, Inst Plant Physiol & Ecol, Shanghai Inst Biol Sci, Shanghai 200233, Peoples R China
3.Shanghai Jiao Tong Univ, Coll Life Sci & Biotechnol, Shanghai 200240, Peoples R China
4.Chinese Acad Sci, Beijing Inst Genom, Beijing 100029, Peoples R China
Recommended Citation
GB/T 7714
Lu, Tingting,Lu, Guojun,Fan, Danlin,et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq[J]. GENOME RESEARCH,2010,20(9):1238-1249.
APA Lu, Tingting.,Lu, Guojun.,Fan, Danlin.,Zhu, Chuanrang.,Li, Wei.,...&Han, Bin.(2010).Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.GENOME RESEARCH,20(9),1238-1249.
MLA Lu, Tingting,et al."Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq".GENOME RESEARCH 20.9(2010):1238-1249.
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