Vaccinium corymbosum GDV RefTrans V1
Materials & Methods
GDV Vaccinium corymbosum RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 39,461 sequences) for Vaccinium corymbosum and provides putative gene function identified by homology to known proteins.
In Vaccinium corymbosum RefTrans V1, 757 million reads from publicly available peer-reviewed Vaccinium corymbosum RNA-Seq data set (Gupta et al. 2015 [SRP039977, SRP039971], LiL et al. 2016 [SRP091871] ) and 22,402 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 by using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTran sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_04) and TrEMBL (UniProtKB/TrEMBL Release 2017_04) protein databases. Information on the top 10 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in GDV together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Vaccinium corymbosum 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.