The relationship between the eight barley transcriptome datasets based on their location on the Barley Pangenome Reference pseudomolecules can be accessed here. You can use this webpage to translate a list of gene IDs to the equivalent locations on the Barley Pangenome Reference pseudomolecules for all other transcriptome datasets.
These comparisons between the various barley transcriptomes were produced by first using GMAP to map the transcriptomes against the Barley Pangenome Reference pseudomolecules and generate locations. The GMAP mapping was run with parameters restricting the results to the single best match with 90% sequence identity and 80% transcript coverage. Then gffcompare was used to compare the GMAP locations of the transcriptomes to the locations of the reference transcript dataset (PanBaRT20 annotation).
The eight barley transcriptomes included here are as follows:
| Dataset | Dataset description | #Transcripts | #Transcripts mapped | Nomenclature example |
|---|---|---|---|---|
| MLOCs | From RNA-seq of 8 tissues mapped to Morex WGS assembly | 154,788 | 143,968 | MLOC_54382.1 |
| JLOCs | From RNA-seq of 16 tissues mapped to Morex WGS assembly | 77,360 | 72,601 | JLOC1_22150.1 |
| HORVUv1 | - | 334,126 | 304,919 | HORVU1Hr1G000020.1 |
| HORVUv3 | - | 83,990 | 78,895 | HORVU.MOREX.r3.1HG0004350.1 |
| BARTv1 | From a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome, 2017 (Published paper). | 177,240 | 167,380 | BART1_0-u00498.001 |
| BARTv2 | Barley RTD based on the Barke genome assembly | 148,260 | 145,220 | BaRT2v18chr1HG009360.2 |
| PanBaRT20 | Barley Pantranscriptome - as part of the Barley Pangenome project | 581,977 | 568,766 | PanBaRT20_chr1HG00001.1 |
| HvMxRTD | Morex Transcriptome RTD - all available Morex RNA-seq mapped to the Morex genome | 149,850 | 149,850 | Hv_Mx_chr1HG07237.1 |