Fragaria x ananassa Camarosa Genome v1.0 Pseudomolecules (unmasked)

Human-Readable NameFragaria x ananassa Camarosa Genome v1.0 Pseudomolecules (unmasked)
Database NameF_ana_Camarosa_6-28-17_unmasked.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Fragaria x ananassa Camarosa Genome v1.0
RegEx/^(\S+).*/
Link-out Typejbrowse
blastp of Fragaria iinumae v1.0 proteins vs NCBI nr
Resource Links: 
View Assembly in JBrowse|https://www.rosaceae.org/jbrowse/index.html?data=data%2Ffragaria%2Ffiinumae_v1.0
BLAST|/blast
View Synteny|/synview/search
Fragaria iinumae Genome v1.0 Assembly & Annotation

Publication

Edger et al. 2019. Reply to 'Revisiting the origin of octoploid strawberry’. accepted to Nature Genetics. 

 

Genome assembly and quality evaluation 

Genome assembly was performed on PacBio long reads using FALCON v0.3.0(GitHub, 2018. Mar 18). Total genome coverage (~172X) before assembly was estimated by total bases from PacBio reads divided by the genome size (265.56 Mb) for F. iinumae. Error correction and preassembly were carried out with the FALCON pipeline after evaluating the outcomes of using different para... [more]

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

The Fragaria iinumae Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) fiinumae-v1.0.fasta.gz

 

The Fragaria iinumae v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) fiinumae-v1.0.proteins.fasta.gz
CDS (FASTA file) fiinumae-v1.0.CDs.fasta.gz
Genes (GFF3 file) fiinumae-v1.0.genes.gff3.gz

 

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

Homology of the Fragaria iinumae 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

Fragaria iinumae v1.0 proteins with NCBI nr homologs (EXCEL file) fiinumae-v1.0_vs_nr.xlsx.gz
Fragaria iinumae v1.0 proteins with NCBI nr (FASTA file) fiinumae-v1.0_vs_nr_hit.fasta.gz
Fragaria iinumae v1.0 proteins without NCBI nr (FASTA file) fiinumae-v1.0_vs_nr_noHit.fasta.gz
Fragaria iinumae v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) fiinumae-v1.0_vs_arabidopsis.xlsx.gz
Fragaria iinumae v1.0 proteins with arabidopsis (Araport11) (FASTA file) fiinumae-v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria iinumae v1.0 proteins without arabidopsis (Araport11) (FASTA file) fiinumae-v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria iinumae v1.0 proteins with SwissProt homologs (EXCEL file) fiinumae-v1.0_vs_swissprot.xlsx.gz
Fragaria iinumae v1.0 proteins with SwissProt (FASTA file) fiinumae-v1.0_vs_swissprot_hit.fasta.gz
Fragaria iinumae v1.0 proteins without SwissProt (FASTA file) fiinumae-v1.0_vs_swissprot_noHit.fasta.gz
Fragaria iinumae v1.0 proteins with TrEMBL homologs (EXCEL file) fiinumae-v1.0_vs_trembl.xlsx.gz
Fragaria iinumae v1.0 proteins with TrEMBL (FASTA file) fiinumae-v1.0_vs_trembl_hit.fasta.gz
Fragaria iinumae v1.0 proteins without TrEMBL (FASTA file) fiinumae-v1.0_vs_trembl_noHit.fasta.gz

 

Functional annotation for the Fragaria iinumae genome v1.0 are available for download below. The Fragaria iinumae 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 fiinumae-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan fiinumae-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways fiinumae-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs fiinumae-v1.0_KEGG-pathways.xlsx.gz

 

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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 Fragaria iinumae 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 Fragaria iinumae_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Fragaria iinumae_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Fragaria iinumae_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Fragaria iinumae_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Fragaria iinumae_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Fragaria iinumae_v1.0_rubus_GDR_reftransV2