Potato genome sequence paper

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