L. culinaris CSFL RefTrans V2
Materials & Methods
CSFL Lens culinaris RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 33,613 sequences) for Lens culinaris and provides putative gene function identified by homology to known proteins.
In Lens culinaris RefTrans V2, 1.1 billion RNA-Seq reads from publicly available, peer-reviewed Lens culinaris RNA-Seq data sets (Sharpe et al. 2013 [SRP019372], Verma et al. 2013 [SRP007008], Yilmaz Temel et al. 2015 [SRP026548], Sudheesh et al. 2016 [SRP092804], Singh et al. 2017 [SRP068600]), and 9,539 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_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 Lens culinaris 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.