Transcriptome Relationships

The relationship between the six barley transcriptome datasets and the BaRT2v18 transcript dataset can be accessed here. You can use this webpage to translate a list of gene IDs to the equivalent BaRT2v18 transcript IDs.

These comparisons between the various barley transcriptomes were produced by first using GMAP to map the transcriptomes against the Barke genome assembly and generate locations. The GMAP mapping was run with parameters restricting the results to the single best match and 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 (BaRT2v18 annotation).

The six barley transcriptomes included here are as follows:

DatasetDataset description#Transcripts#Transcripts mappedNomenclature example
MLOCsFrom RNA-seq of 8 tissues mapped to Morex WGS assembly154,788143,968MLOC_54382.1
JLOCsFrom RNA-seq of 16 tissues mapped to Morex WGS assembly77,36072,601JLOC1_22150.1
BARTv1From a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome, 2017 (Published paper).177,240167,380BART1_0-u00498.001
BARTv2Latest barley RTD based on the Barke genome assembly148,260145,220BaRT2v18chr1HG009360.2

Please paste a list of barley gene IDs - one per line