ArticlePlant methods2020
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the
Article in Plant methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
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- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Global profiling of alternative splicing landscapes in response to cold stress during the cotyledon stage in cotton.BMC genomics · 2026Article
- Next generation sequencing and beyond: a review of genomic sequencing methods.Functional & integrative genomics · 2025Article
- Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs.Briefings in bioinformatics · 2025Article
- Full-Length Transcriptome Sequencing and hsp Gene Family Analysis Provide New Insights into the Stress Response Mechanisms ofBiology · 2025Article
- Transcriptomics data for muscle development in Goats.Scientific data · 2025Article
- The full-length transcriptome analysis of blueberry under different pH conditions.BMC plant biology · 2025Article
- A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.Nature methods · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- High-throughput PacBio library preparation and sequencing techniques for genomic DNA and TNA.Frontiers in genetics · 2025Article
- DNA Sequencing and the Third-Generation Sequencing Revolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Research Progress of Single-Molecule Sequencing and Its Significance in Nucleic Acid Metrology.Biosensors · 2024Review
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense.Molecular genetics and genomics : MGG · 2024Article
- Recent progress in DNA data storage based on high-throughput DNA synthesis.Biomedical engineering letters · 2024Review
- Article
- Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.Plant methods · 2024Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio sequencing, whereas ONT is rarely used. Therefore, in this study, we examined ONT RNA sequencing methods in plants. We performed a detailed evaluation of reads from PacBio, Nanopore direct cDNA (ONT Dc), and Nanopore PCR cDNA (ONT Pc) sequencing including characteristics of raw data and identification of transcripts. In addition, matched Illumina data were generated for comparison.
resultsONT Pc showed overall better raw data quality, whereas PacBio generated longer read lengths. In the transcriptome analysis, PacBio and ONT Pc performed similarly in transcript identification, simple sequence repeat analysis, and long non-coding RNA prediction. PacBio was superior in identifying alternative splicing events, whereas ONT Pc could estimate transcript expression levels.
conclusionsThis paper made a comprehensive comparison of PacBio and nanopore-based RNA sequencing of the
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