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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)