Fragaria vesca Whole Genome v2.0.a1 Assembly & Annotation

Genome Overview
Analysis NameFragaria vesca Whole Genome v2.0.a1 Assembly & Annotation
MethodModification of the assembly of the v. 1.1 using linkage map data
SourceFragaria vesca Whole Genome v1.1 Assembly
Date performed2014-12-04

About the Assembly

The Fragaria vesca genome v2.0.a1 was created by first generating three Fragaria vesca ssp. bracteata linkage maps (Tennessen et al. 2013; Tennessen et al. 2014). The scaffold order and orientation were set to be the same as in the F. vesca v. 1.1. assembly by default, unless there was conflicting evidence from these linkage maps. Scaffolds were broken into distinct sections only if there were multiple polymorphisms on the same scaffold mapping to different locations. Orthologs in the Prunus persica genome assembly were used to guide the locations of scaffold splits and the placement of interchromosome translocations that could not be placed unambiguously based on map position. Two missing scaffolds were also added (scA and scB as described in Tennessen et al. 2013) for a total of 287 scaffolds. The 211.7Mb assembly consists of 7 pseudochromosomes with all polymorphisms in linear order based on their linkage map positions, plus an unassembled pseudochromosome Un.

Publication

Tennessen JA, Govindarajulu R, Ashman TL, Liston A. 2014. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol. 6(12):3295-313. doi: 10.1093/gbe/evu261.

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.rosaceae.org/jbrowse/index.html?data=data/fragaria/fvesca_v2.0.a1&loc=
Assembly

The Fragaria vesca v2.0.a1 genome assembly files are available in FASTA and GFF3 formats.  There are a total of 7 pseudomolecules plus an unassembled pseudomolecule in this assembly of strawberry.

Downloads

Pseudomolecules & Scaffolds (FASTA file)  Fragaria_vesca_v2.0.a1_pseudomolecules.fasta.gz
Pseudomolecules & Scaffolds (GFF3 file)  Fragaria_vesca_v2.0.a1_pseudomolecules.gff3.gz

 

Gene Predictions

The Fragaria vesca v2.0.a1 genome gene prediction files are available in GFF3 format.

Downloads

Genes and transcripts (GFF3 file) Fragaria_vesca_v2.0.a1.transcript.gff3.gz
Alignment of F. vesca v1.1.a2 to F. vesca v2.0 (GFF3 file) Fragaria_vesca_v1.1.a2_on_v2.0_genome.gff3.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.