BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
| Autor: | Micha Bayer, Sarah M. McKim, Wenbin Guo, John L. Fuller, Craig G. Simpson, Paulo Rapazote-Flores, Claus-Dieter Mayer, Pete E. Hedley, Miriam Schreiber, Jason Kam, Monika Zwirek, M. Cristina Casao, Claire Halpin, Jenny Morris, Gordon Stephen, Abdellah Barakate, Robbie Waugh, Runxuan Zhang, John W. S. Brown, Linda Milne |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Gene isoform
0106 biological sciences Untranslated region Differential alternative splicing lcsh:QH426-470 lcsh:Biotechnology RNA-Seq Computational biology Biology 01 natural sciences Transcriptome 03 medical and health sciences Gene Expression Regulation Plant Barley lcsh:TP248.13-248.65 Databases Genetic Exome Sequencing Gene expression Splice junction Genetics Gene Differential gene expression Plant Proteins 030304 developmental biology 2. Zero hunger 0303 health sciences Sequence Analysis RNA Gene Expression Profiling Spliced Genes food and beverages Hordeum Alternative Splicing lcsh:Genetics RNA splicing Reference transcript dataset DNA microarray Research Article 010606 plant biology & botany Biotechnology Reference genome |
| Zdroj: | BMC Genomics, Vol 20, Iss 1, Pp 1-17 (2019) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background The 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. Results A 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. Conclusion A 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
| Nepřihlášeným uživatelům se plný text nezobrazuje | K zobrazení výsledku je třeba se přihlásit. |