The genome of woodland strawberry (Fragaria vesca)

Abstract

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.

Figure 1

Anchoring the F. vesca genome to the diploid Fragaria reference map, FV × FN. Scaffolds representing 198.1 Mb of scaffolded sequence with embedded gaps (99.2% of all contiguous sequence over 10 kb in length) were anchored to the genetic map with 390 genetic markers. Blue scaffolds were anchored and oriented using map positions of markers in the full FV × FN progeny, whereas the yellow scaffolds were anchored to mapping bins.

Figure 2

A schematic representation of the positions of 389 RosCOS markers on the seven pseudochromosomes (FC1-7) of F. vesca in relation to their bin map positions on the eight linkage groups (PG1-8) of the Prunus T × E reference map. The diagram was plotted using Circos; map positions from the Prunus reference map were converted to approximate physical positions for comparison by multiplying the marker positions in cM by 400,000. Markers were spaced at 100,000 nucleotide intervals within each T × E mapping bin (see URLs).

Figure 3

Gene ontology mapping and functional annotation of strawberry genes. Overrepresented gene ontology categories in fruit (a) and root (b) expressed genes. The circles are shaded based on significance level (yellow, false discovery rate < 0.05), and the radius of each circle denotes the number of genes in each category.

Figure 4

Venn diagram showing unique and shared gene families between and among rice, grape, Arabidopsis and strawberry. Comparative analysis with rice, Arabidopsis, grape and strawberry genes revealed that a total of 103,570 genes from those four species were shared among all four species. In the case of strawberry, 18,170 genes of the total 33,264 protein-coding genes (from ab initio predictions; Supplementary Table 5) aligned in 9,895 clusters. Comparison of the four species revealed 681 gene clusters unique to strawberry. There were 663 gene clusters unique to strawberry and Arabidopsis, whereas there were 262 gene clusters unique to rice and strawberry. Additionally, there were 6,233 gene clusters that were shared among all four species. The analysis was done using a total of 21 species to find the clusters.

Figure 5

Maximum likelihood phylogeny relating Fragaria to seven other eudicot genomes with two monocot outgroups. The tree is based on alignments of 154 genes present in at least eight of ten genomes. Genes exhibiting little or no duplication were selected, and duplicates, predominant in Glycine, were removed. Species in the Fabidae clade are colored red and species in the Malvidae clade are colored blue. The placement of Populus in Malvidae and not Fabidae, as found in previous studies, was strongly supported by topology and resampling tests. Bootstrap values are shown at nodes. The scale is amino acid substitutions per site.