Paul Sharp Phytothreats: WP4

Overview of WP4

1. D D d Work package 4 Predicting risk via analysis of Phytophthora genome evolution Paul Sharp (University of Edinburgh) paul.sharp@ed.ac.uk
2. WP4: Phytophthora genome evolution - Understanding UK Phytophthora diversity - Understanding origins of emerging Phytophthora strains - Understanding genome evolution in Phytophthora Adaptation to new hosts? Adaptation to woody hosts? Hybridization? Horizontal gene transfer? Paul Sharp (University of Edinburgh) Sarah Green (Forest Research) David Cooke (James Hutton Institute) Leighton Pritchard
3. Phytophthora genomes: 15,000 – 20,000 genes 37 Mbp (P.kernoviae) to 240 Mbp (P.infestans) Molecular genetics DNA ..TAGAATGGAGGAGGCAGCCGAGATCTCCCGCCCCATGGTG.. | | | | | | | | | | | | protein MetGluGluAlaAlaGluIleSerArgProMetVal.. Phytophthora infestans beta-glucanase 586 amino acids, 1758 bases
4. ..GAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGA... ..GAGGCGCTGTACCTGGTGTGCGGGGAGCGCGGCTTTTTTTATACACCCAAGT... Organisms (animals, plants, bacteria, etc.) share genes, inherited from common ancestors Genes accumulate mutations over time Insulin genes: Human Rabbit 40 identities across 50 sites = 80% identity Molecular evolution
5. x x x x x x x x x x ..GAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGA... ..GAGGCGCTGTACCTGGTGTGCGGGGAGCGCGGCTTTTTTTATACACCCAAGT... Organisms (animals, plants, bacteria, etc.) share genes, inherited from common ancestors Genes accumulate mutations over time Insulin genes: Human Rabbit 10 mutations across 50 sites = 20% difference .. Molecular evolution
6. First observed in 1960s (proteins) Confirmed with DNA sequences in 1980s NB: Slope (rate) varies among genes/proteins 20 15 10 5 0 0 10 20 30 40 50 60 Human v Chimpanzee Opossum v Kangaroo Cow v Sheep Human v Macaque Dog v Cat Cow v Pig Rabbit v Mouse Age of ancestor (Myr ago) % amino acid difference ‐globin Molecular Clock
7. Human: 15% vs Lemur 7% vs Vervet monkey 2% vs Chimpanzee Lemur Vervet Chimpanzee Human 23 million years ago Molecular trees 65-60 7-6
8. Phytophthora trees GRUNWALD et al. (2011) Plant Path. 61:610 P.obscura from Germany and USA P.austrocedrae from Argentina (Austrocedrus chilense) Evolutionary tree from 7 genes
9. Complications .... Hybrids diploid species X diploid species Y Nucleus Chloroplast OR Mitochondrion
10. Complications .... Hybrids Polyploids ! diploid species X diploid species Y tetraploid species Z Nucleus Chloroplast OR Mitochondrion
11. Hybrids (Dryopteris) LEFT: nuclear genes (pgiC) RIGHT: chloroplast genes Adapted from: SESSA, ZIMMER & GIVNISH (2012) Mol.Phyl.Evol. 64:583 Estimated 225-250 species of Dryopteris worldwide 89 species Nuclear gene: pgiC 50 species one copy 26 species had 2 copies 13 species had 3 copies
12. LEFT: nuclear genes (pgiC) RIGHT: chloroplast genes Adapted from: SESSA, ZIMMER & GIVNISH (2012) Mol.Phyl.Evol. 64:583 Estimated 225-250 species of Dryopteris worldwide Hybrids (Dryopteris)
13. LEFT: nuclear genes (pgiC) RIGHT: chloroplast genes Adapted from: SESSA, ZIMMER & GIVNISH (2012) Mol.Phyl.Evol. 64:583 Estimated 225-250 species of Dryopteris worldwide Hybrids (Dryopteris)
14. X = P. reichenowi vs P. gaboni Y = P. falciparum vs P. gaboni Complications .... Horizontal gene transfer Plasmodium parasites of apes from chimpanzees and gorillas SUNDARARAMAN et al. (2016) Nature Comms. 7:11078
15. P. falciparum v P. reichenowi P. falciparum v P. gaboni P. reichenowi v P. gaboni Horizontal gene transfer part of chromosome 4:
16. Horizontal gene transfer EBA165 RH5 normal tree unusual tree
17. NOWELL et al. (2014) Genome Biol. Evol. 6:1514 Tree: 2140 ‘core’ genes Pseudomonas syringae - pathovars found on different hosts Genomes ~ 6Mbp ~6000 genes Complications .... Gene gain/loss
18. Gene gain and loss NOWELL et al. (2014) Genome Biol. Evol. 6:1514 Pseudomonas syringae pan- and core-genomes Number of genomes
19. NOWELL et al. (2014) Genome Biol. Evol. 6:1514 Rates of gain and loss SEEM faster near the tips (transient gains and losses) During 1% AA divergence: 1000s of gains/losses Gene gain and loss
20. NOWELL et al. (2016) Molec.Plant Path. (in press) Genomes of 64 strains 38 from woody hosts 26 others Pseudomonas syringae
21. Genes associated with woody hosts
22. NOWELL et al. (2016) Molec. Plant Path. (in press) Genes gained along the path to Pseudomonas syringae pv. aesculi Gene gains
23. WP4: Phytophthora genome evolution - Understanding UK Phytophthora diversity - Understanding origins of emerging Phytophthora strains - Understanding genome evolution in Phytophthora Adaptation to new hosts? Adaptation to woody hosts? Hybridization? Horizontal gene transfer? Paul Sharp (University of Edinburgh) Sarah Green (Forest Research) David Cooke (James Hutton Institute) Leighton Pritchard