P. sativum CSFL RefTrans V2
Materials & Methods
CSFL Pisum sativum RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 63,990 sequences) for Pisum sativum and provides putative gene function identified by homology to known proteins.
In Pisum sativum RefTrans V2, 2.4 billion RNA-Seq reads from publicly available, peer-reviewed Pisum sativum RNA-Seq data sets (Trujillo et al. 2014 [SRP045233], Sudheesh et al. 2015 [SRP056009,SRP056105], Yendrek et al. 2015 [SRP009826], Susete Alves-Carvalho et al. 2015 [SRP049810], Liu N et al. 2015 [SRP063052], Zhukov VA et al. 2015[SRP058689], Kerr et al. 2017 [SRP068822]) and 18,576 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 Pisum sativum 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.