ArticleThe Plant journal : for cell and molecular biology2022
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 50 citations in OpenAlex.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- Vernalization regulatory network identifies potential novel functions for genes in the HvVRN2 locus.The New phytologist · 2026Article
- Pan-genome analysis reveals hidden diversity and selection signatures of auxin response factors (ARFs) associated with breeding in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Loss of E3 ligase HvST1 function substantially increases distal crossover frequency.The New phytologist · 2026Article
- Genomic basis underlying alternative transcripts-mediated drought tolerance in maize.Genome biology · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue.Annals of botany · 2025Article
- Beyond gene sequences: Pan-transcriptome links transcriptional complexity to functional diversity.Plant communications · 2025Article
- Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves.Scientific reports · 2025Article
- Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos.BMC plant biology · 2025Article
- ABA-induced alternative splicing drives transcriptomic reprogramming for drought tolerance in barley.BMC plant biology · 2025Article
- Genome-wide characterization of two-component system elements in barley enables the identification of grain-specific phosphorelay genes.BMC plant biology · 2025Article
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- Altered expression of a raspberry homologue of VRN1 is associated with disruption of dormancy induction and misregulation of subsets of dormancy-associated genes.Journal of experimental botany · 2024Article
- The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare).Scientific reports · 2024Article
- Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile ofPlants (Basel, Switzerland) · 2024Article
- Genomic resources for a historical collection of cultivated two-row European spring barley genotypes.Scientific data · 2024Article
- Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence.The Plant cell · 2023Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Diversity of gene expression responses to light quality in barley.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 4 countries.
Funding
Abstract
Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.
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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.