ArticleGenome biology2022
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
76 citing papers in PubMed, 111 citations in OpenAlex.
- Article
- Validation of the International Weed Genomics Consortium genome annotation pipeline through reannotation of the model species Arabidopsis thaliana.The plant genome · 2026Article
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Genome-wide mapping of DCP2-dependent 5' cap footprints inNAR genomics and bioinformatics · 2026Article
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- CONSERVATION AND DIVERGENCE WITHIN THEbioRxiv : the preprint server for biology · 2026Article
- Comparative Analysis of Full-Length Reference Gene Stability inPlants (Basel, Switzerland) · 2026Article
- Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.The plant genome · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila.bioRxiv : the preprint server for biology · 2026Article
- Alternative splicing and polyadenylation facilitate transcriptome diversity underlying high-altitude adaptation in pigs.Communications biology · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Differential splicing fine-tunes guard cell gene expression and is required for drought tolerance in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2026Article
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.The EMBO journal · 2026Article
- Highly accurate ab initio gene annotation with ANNEVO.Nature methods · 2026Article
- Full-length transcriptome sequencing analysis and characterization of MADS-box genes in Rhododendron fortunei.BMC plant biology · 2026Article
- Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes.bioRxiv : the preprint server for biology · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
39 authors at 20 institutions in 12 countries.
Funding
Abstract
backgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.
resultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.
conclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.