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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
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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)