BaRTv2: a highly resolved barley reference transcriptome for accurate transcript‐specific RNA‐seq quantification

• DOI: 10.1111/tpj.15871
• Publication Date: 2022-06-15T15:54:54Z
• Authors: Max Coulter; Juan Carlos Entizne; Wenbin Guo; Micha Bayer; Ronja Wonneberger; Linda Milne; Miriam Schreiber; Allison Haaning; Gary J. Muehlbauer; Nicola McCallum; John Fuller; Craig Simpson; Nils Stein; John W. S. Brown; Robbie Waugh; Runxuan Zhang
• Keywords: Resource; 0301 basic medicine; 2. Zero hunger; 570; 0303 health sciences; /dk/atira/pure/subjectarea/asjc/1300/1311; Sequence Analysis, RNA; name=Genetics; Gene Expression Profiling; Iso-seq; /dk/atira/pure/subjectarea/asjc/1100/1110; barley; Hordeum; reference transcript datasets; name=Cell Biology; 03 medical and health sciences; RNA-seq ; Iso-seq ; transcriptomic analysis ; reference transcript datasets ; barley; RNA-Seq; RNA-seq; name=Plant Science; Transcriptome; /dk/atira/pure/subjectarea/asjc/1300/1307; transcriptomic analysis

SUMMARYAccurate 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.