气候变化领域集成服务门户(CCPortal): Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

CCPortal

DOI	10.1101/gr.106120.110
	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
发表日期	2010
ISSN	1088-9051
EISSN	1549-5469
卷号	20 期号:9
英文摘要	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.
学科领域	Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
来源期刊	GENOME RESEARCH
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111600
作者单位	Chinese Acad Sci, Natl Ctr Gene Res, Shanghai 200233, Peoples R China
推荐引用方式 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]. 中国科学院西北生态环境资源研究院,2010,20(9).
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).
MLA	Lu, Tingting,et al."Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq".GENOME RESEARCH 20.9(2010).