2. Fragaria vesca Herbaceous, perennial Genotypic diversity
Reference genomic system for Rosaceae
Robust in vitro regeneration and transformation systems
2n=2x=14
240 Mb
Fragaria x ananassa
2n=8x=56

3. Multiple models for Rosaceae genomics (2008)
In vitro regeneration and transformation systems (2002, 2010)
Molecular karyotype (2004)
cDNA pools (2010)

4. Goals Discover all genes and their functions
Identfy genes critical to valuable horticultural traits
flavor,nutritional value, fowering time etc.
Synteny
Phylogenetic analysis

6. Genome Sequencing and Assembly
Hawaii 4 accession
Sequencing, X39 coverage
Roche/454
Illumina/Solexa
Life Technologies/ SOLID platforms
Over 3,200 scaffolds were assembled with an N50 of 1.3 Mb
Over 95% (209.8 Mb) of total sequence is represented in 272 scaffods
Flow cytometry
~240 Mb

7. Anchoring genome sequence to the genetic map
Scaffolds were anchored to the diploid Fragaria reference linkage map FVxFN
204 genome sequence scaffolds (94% of total scaffold sequence) were anchored to FVXFN map and its associated bin map
By using 390 genetic markers

8. Synteny Macrosyntenic relationships among rosaceous taxa
Prunus X F.vesca
RosCOS markers (389) x 7 pseudochromosomes of F.vesca
‘syntenic blocks’
Ancestral genome for Rosaceae had 9 chromosomes

9. Absence of large duplications Comparison of F.vesca against itself
No evidence of large scale,within genome duplication
Sharing an ancient triplication
Repetitive sequences and transposable elements
Long terminal repeat (LTR) ~16%
CACTA elements 2.8% MITEs 2.4%
LTR retrotransposon family has fewer than 2,100 copies X10,000

10. Transcriptome sequence
Fruit (1,753 genes)
Fruit development genes
Root (2,151 genes)
Transcription factors, kinase and signal transduction
Biotic and abiotic stress-related genes

11. Gene prediction modeling
GeneMark-ES+ identified 34,809 genes
Confirmed the completeness of genome sequence coverage
RNA genes
569 tRNA, 177 rRNA, 111 spliceosomal RNAs, 168 small nuclear RNAs,
76 micro RNA and 24 other RNAs
Chloroplast genome
H4x4 (155,691 bp) encodes 78 proteins, 30 tRNAs and 4 rRNA genes
Absence of atpF group II intron
DNA transfer from plastid to the nuclear genome

12. Strawberry unique gene clusters
33,264 total protein coding genes
18,170 genes aligned in 9,895 clusters .

13. An opportunity for translational studies
Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified.
Transcription factor families
1,616 transcription factors

14. Reinterpretation of angiosperm phylogeny
Fragaria
7 eudicot + 2 monocot
154 genes presented in at least 8/10 genomes

15. Discussion Second smallest sequenced plant genome
Rapidly transformable
Unlike Arabidopsis, Fragaria is perennial.
Having economically important traits

16. Discussion
Plant genome can be sequenced and assembled using short-read technology
Without a physical map or reference genome

17. Fragaria
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies (2012)
Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae) (2013)
Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria (2013)
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution (2013)