Recommended
Recommended
More Related Content
What's hot
What's hot (18)
Viewers also liked
Viewers also liked (19)
Similar to Pulling apart the two genomes of the dikaryotic wheat stripe rust fungus
Similar to Pulling apart the two genomes of the dikaryotic wheat stripe rust fungus (20)
Recently uploaded
Recently uploaded (20)
Pulling apart the two genomes of the dikaryotic wheat stripe rust fungus
- 1. Pulling apart the two genomes of the dikaryotic wheat stripe rust fungus Benjamin Schwessinger DECRA Fellow, Rathjen Lab 14/02/2017
- 2. 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 evolution recombination, somatic hybridization and recombination, TEs, SNPs, … genetic diversity within ’individual’ within populations between strains and populations
- 3. Wheat stripe rust is caused by the heterodikaryotic fungus Puccinia striformis f. sp. tritici Schwessinger 2017, New Phytologist
- 4. A dikaryotic dip-haploid Genome A’ A
- 5. 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
- 6. 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 rates 11dpi 51.21% 47.80% Haplotype information Yes No TE content 50% 25% Estimated Haploid variation ~12% ~0.6% Falcon Unzip Chin et al. 2016, Nature Methods
- 7. A’ A Haploid variation at the nucleotide, gene, and expression level Deletion Insertion Repeats Contraction Expansion Contraction Expansion Tandem ‘duplication’ Nattestad and Schatz 2016, Bioinformatics high nucleotide level diversity
- 8. 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
- 9. 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
- 10. Wheat stripe rust a modern pandemic Schwessinger 2017, New Phytologist
- 11. 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
- 12. Team members and funding At ANU: John Rathjen Ramawatar Nagar Jiheng Hu Veronica Roman Reyna Diana Esperanza Ramirez-Garces Bioinformatics discussion: Sylvain Foret Marcin Adamski Megan McDonald Mogens Hovemoller Annemarie Fejer Justeesen Sajid Ali Robert Park William Cuddy Eric Stone Rob Lanfear
- 13. Stripe rust - a devastating modern pandemic …with fundamental biological questions to answer dikaryotic ureodiniospore adaptation on different hosts sexual vs. asexual evolution recombination, somatic hybridization and recombination, TEs, SNPs, … genetic diversity within ’individual’ within populations between strains and populations Wheat stripe rust as a model spatial separation hosts and sexual vs. asexual reproduction curated high quality collections available dating back 1970s and more amenable to evolutionary studies under controlled environment conditions technological advances in long read sequencing