The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing
文献类型：期刊论文
| 作者 | Zhang, Yue1,3; Nyong'A, Tonny Maraga1,3; Shi, Tao1; Yang, Pingfang2 |
| 刊名 | DNA RESEARCH
 |
| 出版日期 | 2019-08-01 |
| 卷号 | 26期号:4页码:301-311 |
| 关键词 | SMRT sequencing Illumina RNA-seq full length alternative splicing isoform variants |
| ISSN号 | 1340-2838 |
| DOI | 10.1093/dnares/dsz010 |
| 英文摘要 | Alternative splicing (AS) plays a critical role in regulating different physiological and developmental processes in eukaryotes, by dramatically increasing the diversity of the transcriptome and the proteome. However, the saturation and complexity of AS remain unclear in lotus due to its limitation of rare obtainment of full-length multiple-splice isoforms. In this study, we apply a hybrid assembly strategy by combining single-molecule real-time sequencing and Illumina RNA-seq to get a comprehensive insight into the lotus transcriptomic landscape. We identified 211,802 high-quality full-length non-chimeric reads, with 192,690 non-redundant isoforms, and updated the lotus reference gene model. Moreover, our analysis identified a total of 104,288 AS events from 16,543 genes, with alternative 3' splice-site being the predominant model, following by intron retention. By exploring tissue datasets, 370 tissue-specific AS events were identified among 12 tissues. Both the tissue-specific genes and isoforms might play important roles in tissue or organ development, and are suitable for 'ABCE' model partly in floral tissues. A large number of AS events and isoform variants identified in our study enhance the understanding of transcriptional diversity in lotus, and provide valuable resource for further functional genomic studies. |
| 资助项目 | National Natural Science Foundation of China[31700197] ; Key Research Program of Frontier Sciences, CAS[QYZDB-SSW-SMC017] |
| WOS研究方向 | Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:000493011000002 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://202.127.146.157/handle/2RYDP1HH/14815]  |
| 专题 | 中国科学院武汉植物园 |
| 通讯作者 | Shi, Tao; Yang, Pingfang |
| 作者单位 | 1.China Univ Geosci, Wuhan Bot Garden, CAS Key Lab Aquat Bot & Watershed Ecol, CN-430074 Wuhan, Hubei, Peoples R China 2.Hubei Univ, Sch Life Sci, State Key Lab Biocatalysis & Enzyme Engn, Wuhan 430062, Hubei, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Yue,Nyong'A, Tonny Maraga,Shi, Tao,et al. The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing[J]. DNA RESEARCH,2019,26(4):301-311. |
| APA | Zhang, Yue,Nyong'A, Tonny Maraga,Shi, Tao,&Yang, Pingfang.(2019).The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing.DNA RESEARCH,26(4),301-311. |
| MLA | Zhang, Yue,et al."The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing".DNA RESEARCH 26.4(2019):301-311. |
入库方式： OAI收割
来源：武汉植物园
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