Gossypium raimondii CottonGen RefTrans V1

Overview
Analysis NameGossypium raimondii CottonGen RefTrans V1
Methodreftrans (1.0)
Sourceg.raimondii_cottongen_reftransV1
Date performed2016-11-09

Materials & Methods

CottonGen Gossypium raimondiie RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 31,990 sequences) for Gossypium raimondiie and provides putative gene function identified by homology to known proteins.

In  Gossypium raimondiie RefTrans V1, 545 million RNA-Seq reads from publicly available peer-reviewed G. raimondiie RNA-Seq data sets (Renny-Byfield et al, 2015 [SRP017133]; Renny-Byfield et al, 2014 [SRP017168]; Li et al, 2014 [SRP009820]; Rambani et al, 2014 [SRP028270]), and 63,577 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 raimondiie 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.

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Assembly

 
RefTrans in FASTA format  (31,990 sequences) Gossypium raimondiie RefTrans v1 FASTA format 

 

Homology Analysis 

Homology was determined using the BLASTx algorithm with an e-value cutoff of 1.0 e-6 for the Gossypium raimondiie RefTrans V1 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2015_10), TrEMBL(UniProtKB/TrEMBL Release 2015_10).  Only the best match was kept. 

UniProtKB/Swiss-Prot

BLAST of refTrans to Swiss-Prot EXCEL format (74% refTrans with homologies)  Gossypium raimondiie RefTrans v1 vs Swissprot
RefTrans with homologies  FASTA format Gossypium raimondiie RefTrans v1 vs Swissprot_hit
RefTrans without homologies FASTA format Gossypium raimondiie RefTrans v1 vs Swissprot_noHit

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (98% refTrans with homologies) Gossypium raimondiie RefTrans v1 vs TrEMBL
RefTrans with homologies  FASTA format  Gossypium raimondiie RefTrans v1 vs TrEMBL_hit
RefTrans without homologies FASTA format  Gossypium raimondiie RefTrans v1 vs TrEMBL_noHit

 

InterProscan Analysis

InterPro domains and Gene Ontology assignments were made to Gossypium raimondiie RefTrans V1 using InterProScan at the EBI through Blast2GO.
Gene Ontology annotations by RefTrans EXCEL format Gossypium raimondiie RefTrans V1 Gene Ontology annotations
InterPro annotations by RefTrans EXCEL format Gossypium raimondiie RefTrans V1 InterPro annotations

 

Alignments

The alignment tool 'BLAT' was used to map Gossypium raimondiie RefTrans V1 to the Gossypium raimondii (D5) genome JGI assembly v2.0. Alignments with an alignment length of 95% and 90% identify were preserved. 
BLAT of refTrans to D5 EXCEL format Gossypium raimondiie RefTrans V1_D5 genome JGI assembly v2.0