ReviewFrontiers in genetics2019
Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing.
Review in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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Who cites it
93 citing papers in PubMed.
- An engineered nanopore identifies saccharides, amino acids, peptides and ribonucleotides.Nature biotechnology · 2026Article
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- ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits inCurrent issues in molecular biology · 2026Review
- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
- Role of RNA 5‑methylcytosine modification in cancer: Insights from coding and non‑coding RNAs (Review).Molecular medicine reports · 2026Review
- Alternative Splicing in Plant Development and Abiotic Stress Responses: A Multifunctional Regulatory Mechanism.International journal of molecular sciences · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Comprehensive analysis of alternative splicing and transcriptome diversity in apple using long-read sequencing.Frontiers in plant science · 2026Article
- Antibiotic resistance inFrontiers in microbiology · 2026Review
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- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- Epigenomic Transcriptome Regulation of Growth and Development and Stress Response in Cucurbitaceae Plants: The Role of RNA Methylation.Current issues in molecular biology · 2025Review
- Chronic arsenic exposure and hsa-miR-186 overexpression causes transcriptome-wide differential alternative splicing contributing to skin carcinogenesis in human HaCaT cell line.Archives of toxicology · 2025Article
- Epitranscriptomic Regulation of Hepatitis B Virus by RNA 5-Methylcytosine: Functions, Mechanisms, and Therapeutic Potential.Viruses · 2025Review
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Physiological changes and full-length transcriptome of Artemisia sphaerocephala in response to drought stress.BMC plant biology · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.International journal of molecular sciences · 2025Review
- Identification of Genes and Long Non-Coding RNAs Putatively Related toInternational journal of molecular sciences · 2024Article
33 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
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
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