This work package aims to understand genome evolution in Phytophthora by analyzing UK diversity, origins of emerging strains, and mechanisms of adaptation such as hybridization and horizontal gene transfer. The researchers will sequence genomes to understand how Phytophthora adapts to new hosts, woody hosts, and the role of hybridization and gene transfer in evolution.

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)
%aminoaciddifference
‐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
EBA165RH5
normal treeunusual 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