中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 海洋研究所
  3. 中国科学院海洋研究所
  4. 实验海洋生物学重点实验室
Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification

文献类型：期刊论文

作者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
刊名GENOMICS
出版日期2023-11-01
卷号115期号:6页码:13
ISSN号0888-7543
关键词Nemopilema nomurai Pacific biosciences Oxford Nanopore Technologies Venom Jellyfish dermatitis
DOI10.1016/j.ygeno.2023.110709
通讯作者Yu, Huahua(yuhuahua@qdio.ac.cn) ; Li, Pengcheng(pcli@qdio.ac.cn)
英文摘要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.
WOS关键词PROTEIN ; ALIGNMENT ; TOOL
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
语种英语
出版者ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号WOS:001083384900001
源URL[http://ir.qdio.ac.cn/handle/337002/181625]  
专题海洋研究所_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
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.

入库方式： OAI收割

来源：海洋研究所

浏览0
下载0
收藏0
其他版本

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。