V. faba CSFL RefTrans V2
Materials & Methods
CSFL Vicia faba RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 37,378 sequences) for Vicia faba and provides putative gene function identified by homology to known proteins.
In Vicia faba RefTrans V2, 616 million RNA-Seq reads from publicly available, peer-reviewed faba bean RNA-Seq data sets (Suresh et al. 2013 [SRP043650], Ray et al. 2015 [SRP038935], Webb et al. 2015 [SRP033593,SRP033121], Zhang et al. 2015 [ERP009949], Ocaña S et al. 2015 [SRP045955], Arun-Chinnappa and McCurdy. 2015 [SRP055969], Macas et al, 2015 [ERP004630], Cooper et al, 2017 [SRP098697] ), and 20,697 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 2017_06) and TrEMBL (UniProtKB/TrEMBL Release 2017_06) protein databases. Information on the top 10 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in CSFL together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Vicia faba RefTrans V2 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.