Paul Sharp, Leighton Pritchard, David Cooke, Sarah Green

1. Work package 4
Predicting risk via analysis of Phytophthora
genome evolution
Paul Sharp, Leighton Pritchard, David Cooke, Sarah Green

2. 11/18/162
Phytophthora genome evolution
- Understanding UK Phytophthora diversity
- Understanding origins of emerging Phytophthoras
- Understanding genome evolution in Phytophthora
Adaptation to new hosts? Adaptation to woody hosts?
Hybridization? Horizontal gene transfer?

3. 11/18/163
Proposed approach (P. Sharp)
1. Look at the Phytophthora phylogeny
2. Classify species according to pathogenicity, woody-or-not host (and any other
interesting phenotype?)
3. Categorise those species with, and those without genome data
4. Then identify three species that can be contrasted with existing genomes
Not easy because so many unknowns, particularly for newly described species
Which Phytophthoras to target sequence ?

4. 11/18/164
Clade 1 (P. andina, P. infestans, P. parasitica, P. cactorum)
Clade 2 (P. capsici, P. plurivora, P. multivora)
Clade 3 (P. pluvialis, P. taxon totara)
Clade 4 (P. palmivora)
Clade 5 (P. agathidicida)
Clade 6 (P. pinifolia)
Clade 7 (P. alni, P. sojae, P. pisi, P. rubi, P. fragariae,
P. cambivora, P. cinnamomi)
Clade 8 (P. ramorum, P. lateralis, P. cryptogea, P. syringae, P.
austrocedri)
Clade 9 0
Clade 10 (P. kernoviae)
Phytophthora genomes by clade

5. 11/18/165
Infect woody parts of trees;
P. cactorum, P. plurivora, P. multivora,
P. agathidicida, P. alni, P. cambivora,
P. cinnamomi, P. ramorum, P. lateralis,
P. austrocedri, P. kernoviae
Infect foliage of trees;
P. pluvialis, P. taxon totara, P. palmivora,
P. pinifolia, P. syringae
Infect herbaceous (non-woody) plants;
P. andina, P. infestans, P. parasitica,
P. capsici, P. sojae, P. pisi, P. rubi,
P. fragariae, P. cryptogea
Phytophthora genomes by infection phenotype

6. 11/18/166
Narrow vs broad host range ?
ie P. infestans vs P. cinnamomi
Aerial vs root infecting ?
ie P. ramorum vs P. austrocedri
Strong vs weak pathogens ?
ie all current genomes vs ?
Phytophthora genomes by other phenotype ?
 So look for weak pathogen (as regarded to date) to contrast
with already sequenced, economically important pathogens of woody hosts

7. 11/18/167
Clade 7 has for example P. alni, P. cinnamomi and P. cambivora already sequenced
P. europaea as a contrast ?
Proposed genomes to target sequence

8. 11/18/168
Clade 8c has P. ramorum and P. lateralis already sequenced
P. foliorum as a contrast ?
Proposed genomes to target sequence

9. 11/18/169
Clade 2 has P. multivora and P. plurivora already sequenced
P. multivesiculata as a contrast ?
Proposed genomes to target sequence

10. 11/18/1610
OR novel clade 8d has P. austrocedri and P. syringae (genomes in progress)
P. obscura as a contrast ? (very closely related to P. austrocedri)
Proposed genomes to target sequence