Rosa GDR RefTrans V1.0

Overview
Analysis NameRosa GDR RefTrans V1.0
Methodreftrans (1.0)
Sourcerosa_gdr_reftransV1
Date performed2018-12-21

Materials & Methods

GDR Rosa RefTrans V1.0 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 40,539 sequences) for Rosa and provides putative gene function identified by homology to known proteins.

In Rosa RefTrans V1.0,  4.5 billion RNA-Seq reads from publicly available, peer-reviewed Rosa RNA-Seq data sets (Tian et al. 2018 [SRP128235],  Hibrand et al.  2018 [SRP133785],[SRP128461], Liu et al. 2018 [SRP120271], Han et al. 2017 [SRP092271]), and 22,357 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 using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTrans sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2018_04) and TrEMBL (UniProtKB/TrEMBL Release 2018_04) 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 Rosa 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.

Download

 

Assembly

 
RefTrans in FASTA format  (37,378 sequences) Rosa  RefTrans V1.0 FASTA format 

 

Homology Analysis

Homology of the Rosa RefTrans V1.0 was determined by pairwise sequence comparison using the blastx algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

UniProtKB/Swiss-Prot

ExPASy SwissProt (Excel file) (78% refTrans with homologies) Rosa  RefTrans V1.0 vs Swissprot.xlsx.gz
RefTrans with homologies (Fasta file) Rosa RefTrans V1.0 vs Swissprot_hit.fasta.gz
RefTrans without homologies (Fasta file) Rosa  RefTrans V1.0 vs Swissprot_noHit.fasta.gz

UniProtKB/TrEMBL

ExPAS TrEMBL (Excel file) (93% refTrans with homologies) Rosa   RefTrans V1.0 vs TrEMBL.xlsx.gz
RefTrans with homologies (Fasta file) Rosa  RefTrans V1.0 vs TrEMBL_hit.fasta.gz
RefTrans without homologies (Fasta file) Rosa RefTrans V1.0 vs TrEMBL_noHit.fasta.gz

TAIR10 (arabidopsis)

 TAIR10 (arabidopsis) (Excel file) (78% refTrans with homologies) Rosa  RefTrans V1.0 vs TAIR10.xlsx.gz
RefTrans with homologies (Fasta file)  Rosa RefTrans V1.0 vs TAIR10_hit.fasta.gz
RefTrans without homologies (Fasta file) Rosa  RefTrans V1.0 vs TAIR10_noHit.fasta.gz

NCBI nr

NCBI nr (Excel file) (95% refTrans with homologies) Rosa  RefTrans V1.0 vs NCBI nr.xlsx.gz
RefTrans with homologies (Fasta file) Rosa RefTrans V1.0 vs NCBI nr_hit.fasta.gz
RefTrans without homologies (Fasta file) Rosa  RefTrans V1.0 vs NCBI nr_noHit.fasta.gz

 

InterProscan Analysis

InterPro domains and Gene Ontology assignments were made to the Rosa  RefTrans V1.0 using InterProScan at the EBI through Blast2GO.
Gene Ontology annotations by RefTrans (Excel file) Rosa  RefTrans V1.0 Gene Ontology annotations.xlsx.gz
InterPro annotations by RefTrans (Excel file) Rosa  RefTrans V1.0 InterPro annotations.xlsx.gz

 

KEGG Analysis

KEGG pathway and ortholog assignments were made to the Rosa  RefTrans V1.0 using the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main
KEGG pathway annotations by RefTrans (Excel file)  Rosa  RefTrans V1.0 KEGG pathways.xlsx.gz
KEGG ortholog annotations by RefTrans (Excel file) Rosa  RefTrans V1.0 KEGG orthologs.xlsx.gz

 

Alignments

The alignment tool 'BLAT' was used to map the Rosa  RefTrans V1.0 to the genomes,  Alignments with an alignment length of 98% and 95% identify were preserved. 
BLAT of refTrans to the R.chinensis homozygous genome v2.0 (Excel file) Rosa  RefTrans V1.0_R.chinensis homozygous genome v2.0.xlsx.gz  
BLAT of refTrans to the R.chinensis Illumina genome v1.0 (Excel file) Rosa  RefTrans V1.0_R.chinensis Illumina genome v1.0.xlsx.gz 
BLAT of refTrans to the R.chinensis genome v1.0 (Excel file) Rosa  RefTrans V1.0_R.chinensis Genome v1.xlsx.gz 
BLAT of refTrans to the R.multiflora genome.v1.0 (Excel file) Rosa  RefTrans_R.multiflora Genome v1.0.xlsx.gz