This document summarizes research on predicting the risk of Phytophthora species via analysis of their genome evolution. Researchers sequenced the genomes of three less damaging Phytophthora species (P. europaea, P. foliorum, P. obscura) and compared their gene content to more damaging close relatives. They found 40 genes common in pathogenic species but absent in the less pathogenic species, which may be linked to virulence. Analyzing gene content could help predict which newly discovered Phytophthora species are likely to cause damage. The researchers assembled high quality genomes and estimated gene numbers were similar between the three species.

1. Phytothreats WP4
13th November 2019
Predicting risk via analysis of Phytophthora genome evolution
Ewan Mollison, Paul Sharp – University of Edinburgh
Sarah Green – Forest Research
Leighton Pritchard, David Cooke – James Hutton Institute

2. Phytophthora species
• Oomycete pathogens that can cause
serious plant disease
• Over 170 species identified to date and
more being discovered all the time
• Impact can vary greatly between species –
currently impossible to predict – genomes?
P. infestans in potato
P. austrocedri killing juniper in the Lake District
P. ramorum in larch

3. Genomics
What does genomics mean?
‘Genomics’ is the study of the genomes of
organisms.
In modern molecular biology, the genome
is the entirety of an organism's hereditary
information encoded in DNA
Genomics involves determining the entire
DNA sequence of organisms and fine-scale
genetic mapping
Genome sequencing Pae

4. Rationale
• Sequence genomes of three Phytophthora species thought to be less
damaging than close relatives
• Compare genes present in less damaging and highly damaging
Phytophthora species
• Are genes present in damaging species but absent in less damaging
species involved in Phytophthora virulence?
• Ultimately, gene content might help us predict which newly
discovered species are likely to be most damaging

5. Target species
• P. europaea
Associated with European
oak
Closely related to P. alni
which is killing alder
• P. foliorum
Causes leaf blight in azaleas
Closely related to P. ramorum
which is killing larch
• P. obscura
Associated with horse chestnut
and pieris
Closely related to P. austrocedri
which is killing juniper

6. How were these three genomes assembled ?
1
Genome is fragmented
Genome is fragmented Software assembles
overlapping reads into larger
fragments resulting in
complete genome sequence
ACCTG..
CCTTG..
State-of-the-art sequencing machines
generate millions of short sequence reads
CCTTG..
Sequencing machines generate
millions of sequence reads
2 3

7. Genome assembly summary for our three species
P. europaea P. foliorum P. obscura
Total length (Mbp) 76.9 59.1 62.2
No. fragments 39 22 28
% Genome repetitive 35.5 29.0 28.7
No. predicted genes 19,658 19,484 19,441
Completeness estimate 97.9% 97.9% 98.7%
• Very similar counts for
number of genes
• Appear to be very
“complete” assemblies
based on presence of a
set of test genes

8. Gene content differences between P. europaea and other species
• Green circle shows number of genes
in non damaging P. europaea
• Blue circle shows no. genes in
damaging pathogens of woody hosts
• Yellow circle shows no. genes in
damaging pathogens of non-woody
hosts
• In the overlapping regions we can
see how many genes are shared and
how many are unique to each group

9. Gene content differences between P. foliorum, P. obscura and others
• Further analysis shows 40 genes
common to other damaging pathogens
but not present in both P. obscura and
P. foliorum
• These 40 genes might be linked to
virulence
• We can start to unravel which genes
make a Phytophthora virulent
• Gene content could be used to predict
which new species will be damaging

10. Summary
• We have produced three very complete genome assemblies using a new
method
• We have very good estimates of gene content in each species
• A number of genes common to pathogenic Phytophthora species are
“missing” from the less pathogenic species
• Further work will determine if these genes are linked to virulence
• Impact of new Phytophthora species could be predicted by gene content

11. Funding and partners