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

1. Seong-Hyeuk Nam

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. 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. Genome sequence

5. Genome sequence (DM)
• DM genome Illumina data per insert size (26 libraries)
• Assembly statistics (443 superscaffolds >= 349 Kb)

6. Genome sequence (DM)
• Scaffold size

7. Assembly quality assessment
• Nucleotide alignments (Superscaffold and 10 BACs)

8. Genome sequence (RH)
• RH genome Illumina data per insert size
• RH genome 454 data per insert size

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. Genome annotation
• Gene prediction

11. Genome annotation
• Paralogous and orthologous clusters were identified using
OrthoMCL using the predicted proteomes of 11 plant species

12. Genome annotation
• Identification of disease resistance genes
– Pfam
• NBS (NB-ARC)
• TIR
• LRR
– DM assembly were screened using HMMER against Pfam database

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. Transcriptome sequence
• Gene expression

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