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

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.