Comparative analysis of PacBio and ONT RNA sequencing methods for<i> Nemopilema</i><i> Nomurai</i> venom identification

doi:10.1016/j.ygeno.2023.110709

CORC > 海洋研究所 > 中国科学院海洋研究所 > 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
	Ma, Yuzhen 2,3; Li, Jie 1,2,3; Yu, Huahua 2,3; Teng, Lichao 1,2,3; Geng, Hao 1,2,3; Li, Rongfeng 2,3; Xing, Ronge 2,3; Liu, Song 2,3; Li, Pengcheng 2,3
刊名	GENOMICS
	2023-11-01
卷号	115 期号:6 页码:13
关键词	Nemopilema nomurai Pacific biosciences Oxford Nanopore Technologies Venom Jellyfish dermatitis
ISSN号	0888-7543
DOI	10.1016/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.
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关键词	PROTEIN ; ALIGNMENT ; TOOL
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
内容类型	期刊论文
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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Drugs & Bioprod, 1 Wenhai Rd, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, 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.