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Fragaria vesca Herbaceous, perennial 2n=2x=14 240 Mb • Genotypic diversity • Reference genomic system for Rosaceae • Robust in vitro regeneration and transformation systems 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 (a) Fruit (1,753 genes) • Fruit development genes (a) Root (2,151 genes) • Transcription factors, kinase and signal transduction • Biotic and abiotic stressrelated 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 Strawberry 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)