Pulling apart the two genomes of the dikaryotic wheat stripe rust fungus

Benjamin SchwessingerDECRA Fellow, Rathjen Lab

14/02/2017

Stripe rust - a devastating modern pandemic

www.agric.wa.gov.au/PC_92931.html

Wheat stripe rust a modern pandemic

www.agric.wa.gov.au/PC_92931.html

…with fundamental biological questions to answer

Global loss of US$1 billion yearly

During server outbreaks >80% crop loss

Novel virulent isolates

Rapid adaptation to local wheat varieties

dikaryotic ureodiniospore

adaptation on different hosts

sexual vs. asexual evolutionrecombination, somatic hybridization and recombination, TEs, SNPs, …

genetic diversity within ’individual’within populationsbetween strains and populations

Wheat stripe rust is caused by the heterodikaryotic fungus Puccinia striformis f. sp. tritici

Schwessinger 2017, New Phytologist

A dikaryotic dip-haploid Genome

A’

A

Every good long read genome sequencing project starts with high quality DNA

dx.doi.org/10.17504/protocols.io.ewtbfen

Good DNA in = long reads out

~6 months to fix up protocol for high quality DNA extraction

20kb BluePippin Library

Ramaciotti, Sydney

mean read length > 10 kbp

Improved genome assembly in numbers

PST79-PacBio PST130-Illumina

# contigs 99 (+57) vs. 475 29178

Size 79 (+3.6) vs. 73Mbp 67Mbp

Genome mapping rates 97% 88%

RNAseq mapping rates11dpi

51.21% 47.80%

Haplotype information Yes No

TE content 50% 25%

Estimated Haploid variation

~12% ~0.6%

Falcon UnzipChin et al. 2016, Nature Methods

A’ A

Haploid variation at the nucleotide, gene, and expression levelDeletion Insertion

Repeats

Contraction Expansion

Contraction ExpansionTandem‘duplication’

Nattestad and Schatz 2016, Bioinformatics

high nucleotide level diversity

A’ A

Haploid variation at the nucleotide, gene, and expression level

primary contigs (A) haplotigs (A’)

#contigs/size 156/83Mbp 473/73Mbp

#protein coding genes 15949 14321

% (potentially) haplotype specific genes

19% 9%

high protein coding gene level diversity

A’ A

Haploid variation at the nucleotide, gene, and expression level

A’

A

Allele specific expression

RNAseq reads

allele A

allele A

e.g. 11 days post infection ~6% allele specific upregulation

Wheat stripe rust a modern pandemic

Schwessinger 2017, New Phytologist

What is the global variation of Pst on wheat at a whole genome level?

How does Pst evolve during its asexual phase at a whole genome level?

How do the two distinct Pst nuclei interact?

Goals

What’s the genetic variation of Puccinia on barberry in the Himalayan?

Inform plant breading strategies to target ‘essential’ effectors

Team members and funding

At ANU:John RathjenRamawatar NagarJiheng HuVeronica Roman ReynaDiana Esperanza Ramirez-Garces

Bioinformatics discussion: Sylvain ForetMarcin AdamskiMegan McDonald

Mogens HovemollerAnnemarie Fejer JusteesenSajid Ali

Robert ParkWilliam Cuddy

Eric StoneRob Lanfear

Stripe rust - a devastating modern pandemic…with fundamental biological questions to answer

dikaryotic ureodiniospore

adaptation on different hosts

sexual vs. asexual evolutionrecombination, somatic hybridization and recombination, TEs, SNPs, …

genetic diversity within ’individual’within populationsbetween strains and populations

Wheat stripe rust as a model

spatial separation hostsand sexual vs. asexual reproduction

curated high quality collections available dating back 1970s and more

amenable to evolutionary studies undercontrolled environment conditions

technological advances in long readsequencing