Citrus sinensis CGD RefTrans V1
Materials & Methods
CGD Citrus sinensis RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 33,111sequences) for Citrus sinensis and provides putative gene function identified by homology to known proteins.
In Citrus sinensis RefTrans V1, 1.2 billion RNA-Seq reads from publicly available peer-reviewed Citrus sinensis RNA-Seq data set (Coqueiro DS et al, 2015 [SRP047324] , Terol et al, 2015 [ERP005867], Rawat N et al, 2015 [ SRP022979], Yu et al, 2012 [SRP002687]) and 214,598 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 2015_10) and TrEMBL (UniProtKB/TrEMBL Release 2015_10) 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 Citrus sinensis 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