Citrus sinensis CGD RefTrans V1

Overview
Analysis NameCitrus sinensis CGD RefTrans V1
Methodreftrans (v1)
SourceCitrus sinensis CGD RefTrans V1
Date performed2017-02-15

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

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Assembly

 
RefTrans in FASTA format  (33,111 sequences) Citrus sinensis  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 Citrus sinensis 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 (76% refTrans with homologies) Citrus sinensis  RefTrans v1 vs Swissprot
RefTrans with homologies  FASTA format Citrus sinensis RefTrans v1 vs Swissprot_hit
RefTrans without homologies FASTA format Citrus sinensis  RefTrans v1 vs Swissprot_noHit

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (96% refTrans with homologies) Citrus sinensis  RefTrans v1 vs TrEMBL
RefTrans with homologies  FASTA format Citrus sinensis  RefTrans v1 vs TrEMBL_hit
RefTrans without homologies FASTA format Citrus sinensis RefTrans v1 vs TrEMBL_noHit

 

InterProscan Analysis

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

 

KEGG Analysis

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

 

Alignments

The alignment tool 'BLAT' was used to map Citrus sinensis  RefTrans V1 to the Citrus sinensis genome v1.1 (JGI) Alignments with an alignment length of 95% and 90% identify were preserved. 
BLAT of refTrans to Citrus sinensis genome v1.1 EXCEL format Citrus sinensis  RefTrans V1_Citrus sinensis genome v1.1