ArticleNucleic acids research2020
New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 98 citations in OpenAlex.
- RNA m6A methylation fine-tunes the jasmonic acid biosynthesis pathway to modulate plant aging.The Plant cell · 2026Article
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Emerging roles of non-mNature plants · 2026Review
- Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7.Microbial genomics · 2026Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Comprehensive analysis of alternative splicing and transcriptome diversity in apple using long-read sequencing.Frontiers in plant science · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana.Communications biology · 2025Article
- Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy.Nature communications · 2025Article
- Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database.Journal of integrative plant biology · 2025Article
- Exploring the mFunctional & integrative genomics · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- RNA modifications in plant biotic interactions.Plant communications · 2025Review
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- The landscape of fusion transcripts in plants: a new insight into genome complexity.BMC plant biology · 2024Article
- Nanopore direct RNA sequencing reveals NBMC plant biology · 2024Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current 'RNA-sequencing' technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially under-estimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00-6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including six categories of fusion-transcripts that may result from differential RNA processing mechanisms. Aided by the Tombo algorithm, we found an enrichment of m5C modifications in the mobile mRNAs, consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary, ONT DRS offers an advantage in the identification and functional characterization of novel RNA isoforms and RNA base modifications, significantly improving annotation of the A. thaliana genome.
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