BaRTv1.0

BaRTv1.0 provides a comprehensive barley reference transcript dataset to improve accuracy of RNA-seq-based gene expression and alternative splicing analyses.

Key Features:

• High-Quality Reference Dataset: A non-redundant reference transcript dataset assembled from diverse tissues, cultivars, and abiotic treatments and aligned to the barley cv. Morex reference genome.
• Full-Length cDNA Validation: Full-length complementary DNAs (cDNAs) from the barley variety Haruna Nijo were incorporated to benchmark transcript coverage.
• Alternative Splicing Analysis (QUASI): Includes BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) to correct quantification inaccuracies arising from 5' and 3' UTR variation and enable precise measurement of alternatively spliced isoforms.
• Validation through RT-PCR: High-resolution reverse transcription-polymerase chain reaction (RT-PCR) validated alternative splicing in 86 genes across five organs and tissues.
• Comprehensive Gene Models: Contains 60,444 genes and 177,240 transcripts characterized by longer transcript lengths, reduced fragmentation, and improved gene models supported by splice junction reads.

Scientific Applications:

• Gene expression quantification: Accurate quantification of gene expression from barley RNA-seq data across tissues, cultivars, and abiotic treatments.
• Alternative splicing detection: Detection and quantification of alternatively spliced isoforms and comparison of splicing patterns across organs and tissues.
• Benchmarking and validation: Benchmarking of transcript coverage and validation of transcript assemblies using Haruna Nijo full-length cDNAs and RT-PCR results.

Methodology:

Transcripts were assembled from RNA-seq data across multiple barley tissues, cultivars, and abiotic treatments and aligned to the barley cv. Morex reference genome; QUASI was applied to adjust for 5' and 3' UTR variation for improved quantification.