Potato genome sequence paper
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Potato genome sequence paper



20110825 cgc seminar

20110825 cgc seminar
Nature에 실린 감자 지놈 시퀀싱 논문 요약 발표 자료



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    Potato genome sequence paper Potato genome sequence paper Presentation Transcript

    • Seong-Hyeuk Nam
    • Introduction• Potato is … – Occupies a wide eco-geographical range – Unique food crop in producing stolons – Important dietary source – Narrow genetic base from limited germplasm introduction – Inbreeding depression, pests and pathogens (The Irish potato famine) – Elusive evolutionary and developmental mechanisms• Potato is easy to eat, but difficult to study – Autotetraploid (2n = 4x = 48) and high heterozygosity – Barrier to potato improvement using classical breeding approaches• Potato genome sequencing project – Advance in breeding
    • Genome sequence• Genotype – Phureja DM1-3 516 R44 (DM) • Diploid homozygote (derived from a primitive South American cultivar) – Tuberosum RH89-039-16 (RH) • Diploid heterozygote (resembles commercially cultivated tetraploid potato)
    • Genome sequence
    • Genome sequence (DM)• DM genome Illumina data per insert size (26 libraries)• Assembly statistics (443 superscaffolds >= 349 Kb)
    • Genome sequence (DM)• Scaffold size
    • Assembly quality assessment• Nucleotide alignments (Superscaffold and 10 BACs)
    • Genome sequence (RH)• RH genome Illumina data per insert size• RH genome 454 data per insert size
    • Genome annotation• Identification of repetitive sequences – Transposable elements (TEs) identification – TEs were identified at the DNA and protein level • DNA: RepeatMasker + Repbase • Protein: RepeatProteinMask + WuBlastX + TE protein DB – Potato repeat database construction
    • Genome annotation• Gene prediction
    • Genome annotation• Paralogous and orthologous clusters were identified using OrthoMCL using the predicted proteomes of 11 plant species
    • Genome annotation• Identification of disease resistance genes – Pfam • NBS (NB-ARC) • TIR • LRR – DM assembly were screened using HMMER against Pfam database
    • Transcriptome sequence• RNA-Seq – To aid annotation and address a series of biological question – Different stages/tissues/treatments (leaves, roots, flower, stolon, biotic, abiotic) – 32 DM and 16 RH libraries; 31.5 Gb• Mapping (against the DM genome sequence) – 90.2% of DM reads – 88.6% of RH reads
    • Transcriptome sequence• Gene expression
    • Conclusion• Genome sequence of a unique doubled-monoploid potato clone – Overcome the problems associated with genome assembly due to high levels of heterozygosity – A high-quality draft potato genome sequence – New insights into eudicot genome evolution• Combination of data from the RH – Underlie inbreeding depression• The potato genome provides a new resource for use in breeding