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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
2023-11-01
Source PublicationGENOMICS
ISSN0888-7543
Volume115Issue:6Pages:13
Corresponding AuthorYu, Huahua(yuhuahua@qdio.ac.cn) ; Li, Pengcheng(pcli@qdio.ac.cn)
AbstractRecent 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.
KeywordNemopilema nomurai Pacific biosciences Oxford Nanopore Technologies Venom Jellyfish dermatitis
DOI10.1016/j.ygeno.2023.110709
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:001083384900001
PublisherACADEMIC PRESS INC ELSEVIER SCIENCE
WOS KeywordPROTEIN ; ALIGNMENT ; TOOL
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Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/181626
Collection实验海洋生物学重点实验室
Corresponding AuthorYu, Huahua; Li, Pengcheng
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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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