Potato genome sequence paper

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

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Potato genome sequence paper

  1. 1. Seong-Hyeuk Nam
  2. 2. 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
  3. 3. 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)
  4. 4. Genome sequence
  5. 5. Genome sequence (DM)• DM genome Illumina data per insert size (26 libraries)• Assembly statistics (443 superscaffolds >= 349 Kb)
  6. 6. Genome sequence (DM)• Scaffold size
  7. 7. Assembly quality assessment• Nucleotide alignments (Superscaffold and 10 BACs)
  8. 8. Genome sequence (RH)• RH genome Illumina data per insert size• RH genome 454 data per insert size
  9. 9. 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
  10. 10. Genome annotation• Gene prediction
  11. 11. Genome annotation• Paralogous and orthologous clusters were identified using OrthoMCL using the predicted proteomes of 11 plant species
  12. 12. Genome annotation• Identification of disease resistance genes – Pfam • NBS (NB-ARC) • TIR • LRR – DM assembly were screened using HMMER against Pfam database
  13. 13. 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
  14. 14. Transcriptome sequence• Gene expression
  15. 15. 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

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