The relationship between the nine barley transcriptome datasets based on their location on the PanGenome20 pseudomolecules can be accessed here. You can use this webpage to translate a list of gene IDs to the equivalent locations on the PanGenome20 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 PanGenome20 pseudomolecules and generate locations. The GMAP mapping was run with parameters restricting the results to the single best match with 90% sequence identity. Then gffcompare was used to compare the GMAP locations of the transcriptomes to the locations of the reference transcript dataset (EORNA2RTD).
The nine barley transcriptomes included here are as follows:
| Dataset | Dataset description | #Transcripts | #Transcripts mapped with GMAP | Nomenclature example |
|---|---|---|---|---|
| EoRNA2 | Transcriptome created from merging the PanBaRT20, HvMx, and BARTv2 RTD datasets | 653,285 | 653,285 | EoRNA2_chr4H038939 |
| MLOCs | From RNA-seq of 8 tissues mapped to Morex WGS assembly | 154,788 | 153,517 | MLOC_54382.1 |
| JLOCs | From RNA-seq of 16 tissues mapped to Morex WGS assembly | 77,360 | 77,214 | JLOC1_22150.1 |
| HORVUv1 | The Morex v1 gene annotation | 334,126 | 333,672 | HORVU1Hr1G000020.1 |
| HORVUv3 | The Morex v3 gene annotation | 83,990 | 83,959 | 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 | 176,900 | BART1_0-u00498.001 |
| BARTv2 | Barley RTD based on the Barke genome assembly | 148,260 | 147,396 | BaRT2v18chr1HG009360.2 |
| PanBaRT20 | Barley Pantranscriptome - as part of the Barley Pangenome project (Published paper) | 581,977 | 581,977 | PanBaRT20_chr1H00001.1 |
| HvMxRTD | Morex Transcriptome RTD - all available Morex RNA-seq mapped to the Morex genome | 149,850 | 149,827 | Hv_Mx_chr1HG07237.1 |