Rosa GDR RefTrans V1.0
Materials & Methods
GDR Rosa RefTrans V1.0 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 40,539 sequences) for Rosa and provides putative gene function identified by homology to known proteins.
In Rosa RefTrans V1.0, 4.5 billion RNA-Seq reads from publicly available, peer-reviewed Rosa RNA-Seq data sets (Tian et al. 2018 [SRP128235], Hibrand et al. 2018 [SRP133785],[SRP128461], Liu et al. 2018 [SRP120271], Han et al. 2017 [SRP092271]), and 22,357 ESTs, were downloaded from the NCBI Short Read Archive database, the EBI database and the NCBI dbEST database, respectively. The RNA-Seq reads and ESTs were assembled using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTrans sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2018_04) and TrEMBL (UniProtKB/TrEMBL Release 2018_04) protein databases. Information on the top 10 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in GDR together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Rosa RefTrans V1 using InterProScan at the EBI through Blast2GO. The transcriptome and associated annotation are available to download, search by name, keyword (functional description), or mapped location, and view on the genome through JBrowse.