pyrus GDR reftransV1

Human-Readable Namepyrus GDR reftransV1
Database Namepyrus_GDR_reftransV1.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink
Resource Links: 
View Alignment in JBrowse|https://www.rosaceae.org/jbrowse/index.html?data=data%2Fpyrus%2FpZhongai1_v1.0
BLAST|/blast
Search RefTrans|search/genes
Search Sequences|search/features
Pyrus GDR RefTrans V1.0

Materials & Methods

GDR Pyrus RefTrans V1.0 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 63,681 sequences) for Pyrus and provides putative gene function identified by homology to known proteins.

In Pyrus RefTrans V1.0, 4.5 billion RNA-Seq reads from publicly available, peer-reviewed Pyrus RNA-Seq data sets ([more]

Resource Titles: 
Download
Resource Blocks: 

 

Assembly

  
RefTrans in FASTA format  (63,681 sequences) Pyrus  RefTrans V1.0 FASTA format 

 

Homology Analysis

Homology of the Pyrus 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 (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

UniProtKB/Swiss-Prot
ExPASy SwissProt (Excel file) (69% refTrans with homologies) Pyrus  RefTrans V1.0 vs Swissprot.xlsx.gz
RefTrans with homologies (Fasta file) Pyrus RefTrans V1.0 vs Swissprot_hit.fasta.gz
RefTrans without homologies (Fasta file) Pyrus  RefTrans V1.0 vs Swissprot_noHit.fasta.gz

UniProtKB/TrEMBL
ExPAS TrEMBL (Excel file) (88% refTrans with homologies) Pyrus   RefTrans V1.0 vs TrEMBL.xlsx.gz
RefTrans with homologies (Fasta file) Pyrus  RefTrans V1.0 vs TrEMBL_hit.fasta.gz
RefTrans without homologies (Fasta file) Pyrus RefTrans V1.0 vs TrEMBL_noHit.fasta.gz

Araport11 (arabidopsis)
 Araport11 (arabidopsis) (Excel file) (74% refTrans with homologies) Pyrus  RefTrans V1.0 vs Araport11.xlsx.gz
RefTrans with homologies (Fasta file)  Pyrus RefTrans V1.0 vs Araport11_hit.fasta.gz
RefTrans without homologies (Fasta file) Pyrus  RefTrans V1.0 vs Araport11_noHit.fasta.gz

NCBI nr
NCBI nr (88% refTrans with homologies) Pyrus  RefTrans V1.0 vs NCBI nr.xlsx.gz
RefTrans with homologies (Fasta file) Pyrus RefTrans V1.0 vs NCBI nr_hit.fasta.gz
RefTrans without homologies (Fasta file) Pyrus  RefTrans V1.0 vs NCBI nr_noHit.fasta.gz

 

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

 

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

 

Alignments
The alignment tool 'BLAT' was used to map the Pyrus  RefTrans V1.0 to the genome.  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) Pyrus  RefTrans V1.0_Pussuriensis x communis Zhongai 1 genome v1.0.xlsx.gz  

 

Pyrus ussuriensis x communis Zhongai 1 genome v1.0 cds

Human-Readable NamePyrus ussuriensis x communis Zhongai 1 genome v1.0 cds
Database NamePyrus_ussuriensis_x_communis_Zhongai1-v1.0.cds.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink

Pyrus ussuriensis x communis Zhongai 1 genome v1.0 proteins

Human-Readable NamePyrus ussuriensis x communis Zhongai 1 genome v1.0 proteins
Database NamePyrus_ussuriensis_x_communis_Zhongai1-v1.0.proteins.faa
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for Pyrus ussuriensis x communis Zhongai 1 v1.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Pyrus ussuriensis x communis Zhongai 1 genome v1.0

Human-Readable NamePyrus ussuriensis x communis Zhongai 1 genome v1.0
Database NamePyrus_ussuriensis_x_communis_Zhongai1-v1.0.genome.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Pyrus ussuriensis x communis Zhongai 1 v1.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse
Pyrus ussuriensis x communis ()
Resource Links: 
View Alignment in JBrowse|https://www.rosaceae.org/jbrowse/index.html?data=data/pyrus/pZhongai1_v1.0
BLAST|/blast
Pyrus ussuriensis x communis Zhongai 1 v1.0 Whole Genome Assembly & Annotation

Publication:

Ou C, Wang F, Wang J, Li S, Zhang Y, Fang M, Ma L, Zhao Y, Jiang S. A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. Scientific data. 2019 Nov 25; 6(1):281.

Overview:

'Zhongai 1' [(Pyrus ussuriensis × communis) × spp.] is an excellent pear dwarfing rootstock common in China. It is dwarf itself and has high dwarfing efficiency on most of main Pyrus cultivated species when used as inter-stock. Here we describe the draft genome sequences of 'Zhongai 1' which was assembled using PacBio long reads, Illumina short reads and Hi-C techn... [more]

Resource Titles: 
Assembly
Gene Predictions
Download
Homology
Functional Analysis
Transcript Alignments
Resource Blocks: 

The Pyrus ussuriensis x communis Zhongai 1 Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pZhongai1_v1.0.fasta.gz

 

The Pyrus ussuriensis x communis Zhongai 1 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pZhongai1_v1.0.proteins.fasta.gz
CDS (FASTA file) pZhongai1_v1.0.CDs.fasta.gz
Genes (GFF3 file) pZhongai1_v1.0.genes.gff3.gz

 

All assembly and annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links to download.  Alternatively, you can browse all available files on the FTP repository.

Homology of the Pyrus ussuriensis x communis Zhongai 1 genome v1.0 proteins was determined by pairwise sequence comparison using the blastp 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 (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with NCBI nr homologs (EXCEL file) pZhongai1_v1.0_vs_nr.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with NCBI nr (FASTA file) pZhongai1_v1.0_vs_nr_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without NCBI nr (FASTA file) pZhongai1_v1.0_vs_nr_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pZhongai1_v1.0_vs_arabidopsis.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with arabidopsis (Araport11) (FASTA file) pZhongai1_v1.0_vs_arabidopsis_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without arabidopsis (Araport11) (FASTA file) pZhongai1_v1.0_vs_arabidopsis_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with SwissProt homologs (EXCEL file) pZhongai1_v1.0_vs_swissprot.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with SwissProt (FASTA file) pZhongai1_v1.0_vs_swissprot_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without SwissProt (FASTA file) pZhongai1_v1.0_vs_swissprot_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with TrEMBL homologs (EXCEL file) pZhongai1_v1.0_vs_trembl.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with TrEMBL (FASTA file) pZhongai1_v1.0_vs_trembl_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without TrEMBL (FASTA file) pZhongai1_v1.0_vs_trembl_noHit.fasta.gz

 

Functional annotation for the Pyrus ussuriensis x communis Zhongai 1 genome v1.0 are available for download below. The Pyrus ussuriensis x communis Zhongai 1 genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan pZhongai1_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pZhongai1_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pZhongai1_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pZhongai1_v1.0_KEGG-pathways.xlsx.gz

 

Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Pyrus ussuriensis x communis Zhongai 1 genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.

 

Fragaria x ananassa GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pyrus ussuriensis x communis Zhongai 1_v1.0_rubus_GDR_reftransV2