Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
| Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification | |
Ma, Yuzhen1,2; Li, Jie1,2,3 ; Yu, Huahua1,2; Teng, Lichao1,2,3; Geng, Hao1,2,3; Li, Rongfeng1,2; Xing, Ronge1,2; Liu, Song1,2; Li, Pengcheng1,2
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| 2023-11-01 | |
| 发表期刊 | GENOMICS
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| ISSN | 0888-7543 |
| 卷号 | 115期号:6页码:13 |
| 通讯作者 | Yu, Huahua(yuhuahua@qdio.ac.cn) ; Li, Pengcheng(pcli@qdio.ac.cn) |
| 摘要 | Recent studies on marine organisms have made use of third-generation sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these specialized bioinformatics tools have different algorithmic designs and performance capabilities, they offer scalability and can be applied to various datasets. We investigated the effectiveness of PacBio and ONT RNA sequencing methods in identifying the venom of the jellyfish species Nemopilema nomurai. We conducted a detailed analysis of the sequencing data from both methods, focusing on key characteristics such as CD, alternative splicing, long-chain noncoding RNA, simple sequence repeat, transcription factor, and functional transcript annotation. Our findings indicate that ONT generally produced higher raw data quality in the transcriptome analysis, while PacBio generated longer read lengths. PacBio was found to be superior in identifying CDs and long-chain noncoding RNA, whereas ONT was more cost-effective for predicting alternative splicing events, simple sequence repeats, and transcription factors. Based on these results, we conclude that PacBio is the most specific and sensitive method for identifying venom components, while ONT is the most cost-effective method for studying venogenesis, cnidocyst (venom gland) development, and transcription of virulence genes in jellyfish. Our study has implications for future sequencing technologies in marine jellyfish, and highlights the power of full-length transcriptome analysis in discovering potential therapeutic targets for jellyfish dermatitis. |
| 关键词 | Nemopilema nomurai Pacific biosciences Oxford Nanopore Technologies Venom Jellyfish dermatitis |
| DOI | 10.1016/j.ygeno.2023.110709 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | National Natural Science Foundation of China[41776163] ; National Natural Science Foundation of China[41876164] ; National Key R&D Program of China[2017YFE0111100-04] ; National Key R&D Program of China[2019YFC0312605] |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS类目 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS记录号 | WOS:001083384900001 |
| 出版者 | ACADEMIC PRESS INC ELSEVIER SCIENCE |
| WOS关键词 | PROTEIN ; ALIGNMENT ; TOOL |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/181626 |
| 专题 | 实验海洋生物学重点实验室 |
| 通讯作者 | Yu, Huahua; Li, Pengcheng |
| 作者单位 | 1.Chinese Acad Sci, Ctr Ocean Mega Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 2.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Drugs & Bioprod, 1 Wenhai Rd, Qingdao 266237, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 第一作者单位 | 中国科学院海洋研究所 |
| 通讯作者单位 | 中国科学院海洋研究所 |
| 推荐引用方式 GB/T 7714 | Ma, Yuzhen,Li, Jie,Yu, Huahua,et al. Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification[J]. GENOMICS,2023,115(6):13. |
| APA | Ma, Yuzhen.,Li, Jie.,Yu, Huahua.,Teng, Lichao.,Geng, Hao.,...&Li, Pengcheng.(2023).Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification.GENOMICS,115(6),13. |
| MLA | Ma, Yuzhen,et al."Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification".GENOMICS 115.6(2023):13. |
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| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| 1-s2.0-S088875432300（5440KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
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