C. arietinum CSFL RefTrans V2
Materials & Methods
CSFL Cicer arietinum RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 56,176 sequences) for Cicer arietinum and provides putative gene function identified by homology to known proteins.
In Cicer arietinum RefTrans V2, 1.0 billion RNA-Seq reads from publicly available, peer-reviewed Cicer arietinum RNA-Seq data sets (Jain et al, 2015 [SRP062857], Garg et al, 2016 [SRP059919, SRP059951], Gupta et al, 2017 [SRP041784], Pandey et al, 2017 [SRP078184]), and 52,788 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_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 Cicer arietinum 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.