Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa

doi:10.1186/1471-2164-14-689

CORC > 中国农业科学院 > 蔬菜花卉研究所

	Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa
	Tong, Chaobo 1; Wang, Xiaowu 2; Yu, Jingyin 1; Wu, Jian 2; Li, Wanshun 3; Huang, Junyan 1; Dong, Caihua 1; Hua, Wei 1; Liu, Shengyi 1
刊名	BMC GENOMICS
	2013
卷号	14 页码:-
关键词	Brassica rapa RNA-seq Alternative splicing Transcriptome
ISSN号	1471-2164
DOI	10.1186/1471-2164-14-689
通讯作者	Tong, Chaobo
英文摘要	Background: The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of whole genome sequence of B. rapa, it is essential to further determine the activity of all functional elements of the B. rapa genome and explore the transcriptome on a genome-wide scale. Here, RNA-seq data was employed to provide a genome-wide transcriptional landscape and characterization of the annotated and novel transcripts and alternative splicing events across tissues.Results: RNA-seq reads were generated using the Illumina platform from six different tissues (root, stem, leaf, flower, silique and callus) of the B. rapa accession Chiifu-401-42, the same line used for whole genome sequencing. First, these data detected the widespread transcription of the B. rapa genome, leading to the identification of numerous novel transcripts and definition of 5'/3' UTRs of known genes. Second, 78.8% of the total annotated genes were detected as expressed and 45.8% were constitutively expressed across all tissues. We further defined several groups of genes: housekeeping genes, tissue-specific expressed genes and co-expressed genes across tissues, which will serve as a valuable repository for future crop functional genomics research. Third, alternative splicing (AS) is estimated to occur in more than 29.4% of intron-containing B. rapa genes, and 65% of them were commonly detected in more than two tissues. Interestingly, genes with high rate of AS were over-represented in GO categories relating to transcriptional regulation and signal transduction, suggesting potential importance of AS for playing regulatory role in these genes. Further, we observed that intron retention (IR) is predominant in the AS events and seems to preferentially occurred in genes with short introns.Conclusions: The high-resolution RNA-seq analysis provides a global transcriptional landscape as a complement to the B. rapa genome sequence, which will advance our understanding of the dynamics and complexity of the B. rapa transcriptome. The atlas of gene expression in different tissues will be useful for accelerating research on functional genomics and genome evolution in Brassica species.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; GENETICS & HEREDITY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000326175200002
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101875]
专题	蔬菜花卉研究所
作者单位	1.Chinese Acad Agr Sci, Minist Agr, Oil Crops Res Inst, Key Lab Biol & Genet Improvement Oil Crops, Wuhan 430062, Peoples R China 2.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Key Lab Biol & Genet Improvement Hort Crops, Minist Agr, Beijing 10081, Peoples R China 3.Beijing Genome Inst Shenzhen, Shenzhen 518083, Peoples R China
推荐引用方式 GB/T 7714	Tong, Chaobo,Wang, Xiaowu,Yu, Jingyin,et al. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa[J]. BMC GENOMICS,2013,14:-.
APA	Tong, Chaobo.,Wang, Xiaowu.,Yu, Jingyin.,Wu, Jian.,Li, Wanshun.,...&Liu, Shengyi.(2013).Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa.BMC GENOMICS,14,-.
MLA	Tong, Chaobo,et al."Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa".BMC GENOMICS 14(2013):-.