Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification

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 scalabili...

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Published in:Genomics (San Diego, Calif.) Calif.), 2023-11, Vol.115 (6), p.110709, Article 110709
Main Authors: Ma, Yuzhen, Li, Jie, Yu, Huahua, Teng, Lichao, Geng, Hao, Li, Rongfeng, Xing, Ronge, Liu, Song, Li, Pengcheng
Format: Article
Language:English
Subjects:
Animals
Cnidarian Venoms
High-Throughput Nucleotide Sequencing - methods
Jellyfish dermatitis
Nemopilema nomurai
Oxford Nanopore Technologies
Pacific biosciences
RNA
RNA, Untranslated
Scyphozoa
Sequence Analysis, RNA
Venom
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Summary: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. [Display omitted] •We made a comparison of Pacific Biosciences and Oxford Nanopore Technologies of the Nemopilema nomurai tentacles.•Pacific Biosciences generated better quality in transcript and lncRNA identification.•Oxford Nanopore Technologies performed well in alternative splicing, simple sequence repeat, and transcription factor.•Pacific Biosciences could provide more virulence factors and exact targets for the treatment of jellyfish dermatitis.•Oxford Nanopore Technologies is more cost-effective for exploring venogenesis, cnidocyst development in jellyfish.
ISSN:0888-7543
1089-8646
1089-8646
DOI:10.1016/j.ygeno.2023.110709