Malus x domestica GDR RefTrans V1
Materials & Methods
GDR Malus x domestica RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 85,918 sequences) for Malus x domestica and provides putative gene function identified by homology to known proteins.
In malus x domestica RefTrans V1, 2.1 billion RNA-Seq reads from publicly available peer-reviewed Malus x domestica RNA-Seq data sets (Legay et al, 2015 [SRP046086], Johnson et al, 2015 [SRP048684], Petersen et al, 2015 [ERP005688, ERP002576], Ke et al, 2014 [SRP034726], Gusberti et al, 2013 [ERP003589], Xia et al, 2012 [SRP034165], Kim et al, 2012 [SRP034165])and 326,941ESTs, were downloaded from the NCBI Short Read Archive 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 2015_10) and TrEMBL (UniProtKB/TrEMBL Release 2015_10) 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 Malus x domestica 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.