Fragaria vesca Whole Genome v1.1 Assembly & Annotation

Genome Overview
Analysis NameFragaria vesca Whole Genome v1.1 Assembly & Annotation
MethodManual editing of contigs
SourceFragaria vesca Whole Genome v1.0 Assembly
Date performed2011-04-14

About the Assemblies
This assembly contains an updated pseudomolecule assembly of the original v1.0 (build 8) assembly.  Currently, annotations are not as rich as for the v1.0 build but the assembly includes a improvement in the ordering and placement of contigs.   Annotations will be added as they become available. 

Note:  A correction has been made to the positions of some genes mapped to the v1.1 assembly.  If you have downloaded files for the v1.1 assembly prior to July 20, 2011 please download the most recent.  Corrections have also been made in GBrowse.

Click to view the original v1.0 assembly.

 
Publication for the v1.0 (build 8) assembly.
Shulaev, et. al.  The genome of woodland strawberry (Fragaria vesca).  Nature genetics. 43, 109-116. 2010

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
Assembly

The Fragaria vesca v1.1 genome assembly contains updates to the scaffolds and pseudomolecules.  

This assembly is currently viewable in GBrowse.

Downloads

Pseudomolecules (GFF3 file)  fvesca_v1.1_lg.gff3.gz
Pseudomolecules (FASTA file)  fvesca_v1.1_pseudo.fna.gz
Scaffolds (FASTA file)  fvesca_v1.1_scaffolds.fna.gz
Mapping of scaffolds to pseudomolecules (GFF3 file)  fvesca_v1.1_scaffolds2pseudo.gff3.gz
Non anchored scaffolds (FASTA file)  fvesca_v1.1_unanchored.fna.gz
Chromosome 1 (FASTA file)  fvesca_v1.1_LG1.fna.gz
Chromosome 2 (FASTA file)  fvesca_v1.1_LG2.fna.gz
Chromosome 3 (FASTA file)  fvesca_v1.1_LG3.fna.gz
Chromosome 4 (FASTA file)  fvesca_v1.1_LG4.fna.gz
Chromosome 5 (FASTA file)  fvesca_v1.1_LG5.fna.gz
Chromosome 6 (FASTA file)  fvesca_v1.1_LG6.fna.gz
Chromosome 7 (FASTA file)  fvesca_v1.1_LG7.fna.gz

 

Gene Predictions

Currently there are no new gene predictions for version 1.1 of the genome assembly.  Gene models visible within GBrowse are those from v1.0 superimposed onto v1.1.  A GFF3 file indicating the positions of these gene models can be found below.  For FASTA sequence files for these gene models, please see the v1.0 assembly.  

Downloads

GeneMark hybrid genes (GFF3 file) fvesca_v1.1_genemark_hybrid.gff3.gz

 

Chloroplast

The Fragaria vesca v1.1 chloroplast assembly initially contained no changes between the v1.0 and v1.1 assemblies. However, a correction to the chloroplast sequence has been made since the first release of version v1.1.  The first 33bp were misassembled mtDNA and were removed.  The corrected FASTA and GFF files are provided below as version v1.1-r1.  However, updates have not yet been made to Genbank so the original v1.1 GenBank file provided below contains the previous gene positions.

Downloads

Chloroplast genes (corrected GFF3 file) fvesca_v1.1-r1_chloroplast.gff3.gz
Chloroplast genes (Genbank file)         fvesca_v1.1_chloroplast.gb.gz
Chloroplast sequence v1.1-r1 (FASTA file) fvesca_v1.1-r1_chloroplast.fna.gz

 

Downloads

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.