Fragaria ananassa GDR RefTrans V1
Materials & Methods
GDR Fragaria x ananassa RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 74,947 sequences) for Fragaria x ananassa and provides putative gene function identified by homology to known proteins.
In Fragaria x ananassa RefTrans V1, 5.7 billion RNA-Seq reads from publicly available peer-reviewed Fragaria x ananassa RNA-Seq data sets (Bassil et al, 2015 [SRP044273], Chambers et al. 2014; Pillet et al. 2015 [SRP039356], Li et al, 2015 [SRP049736], Monden et al, 2014 [DRP002812], Sanchez-Sevilla et al. 2014 [ERP004845], Xu et al. 2013 [SRP026142])and 10855 ESTs, 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 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 GDR together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Fragaria x ananassa 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.