Gossypium hirsutum CottonGen RefTrans V1
Materials & Methods
CottonGen Gossypium hirsutum RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 93,449 sequences) for Gossypium hirsutum and provides putative gene function identified by homology to known proteins.
In Gossypium hirsutum RefTrans V1, 2.76 billion RNA-Seq reads from publicly available peer-reviewed G. hirsutum RNA-Seq data sets (Ma et al. 2016 [SRP049434], Bedre et al. 2015 [SRP055046], Li et al. 2015 [SRP055709], Naoumkina et al. 2015 [SRP052863], Wang et al. 2015 [SRP010021] , Fang et al. 2014 [SRP047139], Naoumkina et al. 2014 [SRP026301], Xiao et al. 2014 [SRP033354], Yoo and Wendel. 2014 [SRP017061], Zhang et al. 2014 [SRP012138], Zhang et al. 2014 [SRP041153], Yang et. 2014 [SRP042128], Bowman et al. 2013 [SRP026618], Chen et al. 2013 [SRP030288], Jiao et al. 2013 [SRP026000], Sun et al. 2013 [SRP011398]), and 337,811 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 25 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in CottonGen together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Gossypium hirsutum 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.