Fragaria ananassa GDR RefTrans V1

Overview
Analysis NameFragaria ananassa GDR RefTrans V1
Methodreftrans (v1)
SourceFragaria ananassa GDR RefTrans V1
Date performed2017-07-21

Materials & Methods

GDR Fragaria x ananassa RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 74,947 sequences) for Fragaria x ananassa and provides putative gene function identified by homology to known proteins.

In Fragaria x ananassa RefTrans V1, 5.7 billion RNA-Seq reads from publicly available peer-reviewed Fragaria x ananassa RNA-Seq data sets (Bassil et al, 2015 [SRP044273], Chambers et al. 2014; Pillet et al. 2015 [SRP039356], Li et al, 2015 [SRP049736], Monden et al, 2014 [DRP002812], Sanchez-Sevilla et al. 2014 [ERP004845], Xu et al. 2013 [SRP026142])and 10855 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_04) and TrEMBL (UniProtKB/TrEMBL Release 2017_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 Fragaria x ananassa 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  (74,947 sequences) Fragaria ananassa  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 Fragaria ananassa RefTrans V1 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_04), TrEMBL(UniProtKB/TrEMBL Release 2017_04).  Only the best match was kept. 

UniProtKB/Swiss-Prot

BLAST of refTrans to Swiss-Prot EXCEL format (55% refTrans with homologies) Fragaria ananassa  RefTrans V1 vs Swissprot
RefTrans with homologies  FASTA format Fragaria ananassa RefTrans V1 vs Swissprot_hit
RefTrans without homologies FASTA format Fragaria ananassa  RefTrans V1 vs Swissprot_noHit

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (78% refTrans with homologies) Fragaria ananassa   RefTrans V1 vs TrEMBL
RefTrans with homologies  FASTA format Fragaria ananassa  RefTrans V1 vs TrEMBL_hit
RefTrans without homologies FASTA format Fragaria ananassa RefTrans V1 vs TrEMBL_noHit

 

InterProscan Analysis

InterPro domains and Gene Ontology assignments were made to Fragaria ananassa  RefTrans V1 using InterProScan at the EBI through Blast2GO.
Gene Ontology annotations by RefTrans EXCEL format  Fragaria ananassa  RefTrans V2 Gene Ontology annotations
InterPro annotations by RefTrans EXCEL format Fragaria ananassa  RefTrans V2 InterPro annotations

 

KEGG Analysis

KEGG pathway and ortholog assignments were made to Fragaria ananassa  RefTrans V1 using the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main
KEGG pathway annotations by RefTrans EXCEL format Fragaria ananassa  RefTrans V2 KEGG pathways
KEGG ortholog annotations by RefTrans EXCEL format Fragaria ananassa  RefTrans V2 KEGG orthologs

 

Alignments

The alignment tool 'BLAT' was used to map Fragaria ananassa  RefTrans V1 to the Fragaria_x_ananassa_Reference_Genome_v1.0 Alignments with an alignment length of 95% and 90% identify were preserved. 
BLAT of refTrans to Fragaria x ananassa Reference Genome_v1.0 EXCEL format Fragaria_ananassa  RefTrans V1_vs_f. x.ananassa_Reference Genome_v1.0