ArticleBMC genomics2019
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- The RAD51 paralogue HvXRCC2 affects meiosis and recombination in barley.Journal of experimental botany · 2026Article
- Vernalization regulatory network identifies potential novel functions for genes in the HvVRN2 locus.The New phytologist · 2026Article
- Brassinosteroids negatively regulate barley deacclimation tolerance via modulation of chloroplast gene expression and cell hydration.Scientific reports · 2025Article
- Genetic analysis of the single internode dwarf 1 mutant in barley.BMC plant biology · 2025Article
- Barley resistance and susceptibility to fungal cell entry involve the interplay of ROP signaling with phosphatidylinositol-monophosphates.The Plant journal : for cell and molecular biology · 2025Article
- Genetic and physical localization of a leaf rust susceptibility gene in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- PHOTOPERIOD 1 enhances stress resistance and energy metabolism to promote spike fertility in barley under high ambient temperatures.Plant physiology · 2025Article
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- Article
- Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley (Journal of agricultural and food chemistry · 2024Article
- The Hessian fly resistance gene HvRHF1 is localized in an NBS-LRR gene cluster in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genetic and physical localization of a major susceptibility gene to Pyrenophora teres f. maculata in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- BarleyExpDB: an integrative gene expression database for barley.BMC plant biology · 2023Article
- Natural variation inFrontiers in plant science · 2023Article
- Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Frontiers in plant science · 2023Article
- The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.The Plant journal : for cell and molecular biology · 2022Article
- A SQUAMOSA promoter binding protein-like transcription factor controls crop ideotype for high productivity in barley.Plant direct · 2022Article
- The value of genotype-specific reference for transcriptome analyses in barley.Life science alliance · 2022Article
- BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.The Plant journal : for cell and molecular biology · 2022Article
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20 authors.
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Abstract
backgroundThe time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.
resultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage.
conclusionA high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.
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