2012 Bioinformatics workshop

1. Funding Acknowledgements
• National Science Foundation
– Research Coordination Networks in Biology
– Oomycete Genomics Research Collaboration Network
– 2007-2012
• USDA CSREES
– Microbial Genome Sequencing Program
– Phytophthora parasitica Genome Sequence
– 2010-2013
• USDA NIFA
– Oomycete Coordinated Agricultural Project
– Integrated management of oomycete diseases of soybean and
other crop plants
– 2011-2016

2. Oomycete Genomics, Past, Present and
Future
Brett Tyler
Center for Genome Research and Biocomputing
Oregon State University
and
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University

3. Some Phytophthora hosts
Phytophthora alfalfa larch
Genome almond
apple
macadamia
melon
apricot
Sequencing mustard
avocado oak
azalea oil palm
banana papaya
> 120 destructive bean (Phaseolus) passionfruit
pathogen species blackberry pea (Pisum)
blueberry peach
Brassica pear
Sequenced cabbage pecan
In progress cacao pepper
canola periwinkle
cantaloupe pine
carnation pineapple
cauliflower pistachio
cedar plum
chestnut pomegranate
chickpea potato
citrus pumpkin
clover raspberry
coconut rhododendron
coffee safflower
cotton sesame
cowpea soybean
cranberry squash
cucurbits strawberry
date palm sugar beet
egg plant sunflower
eucalyptus tobacco
fir tomato
guava viburnum
hibiscus walnut
hops zucchini

4. Some Phytophthora hosts
Phytophthora alfalfa larch
Genome almond
apple
macadamia
melon
apricot
Sequencing mustard
avocado oak
azalea oil palm
banana papaya
> 120 destructive bean (Phaseolus) passionfruit
pathogen species blackberry pea (Pisum)
blueberry peach
Brassica pear
Sequenced cabbage pecan
In progress cacao pepper
canola periwinkle
New initiative with BGI cantaloupe pine
(eventually all species) carnation pineapple
cauliflower pistachio
cedar plum
chestnut pomegranate
chickpea potato
citrus pumpkin
clover raspberry
coconut rhododendron
coffee safflower
cotton sesame
cowpea soybean
cranberry squash
cucurbits strawberry
date palm sugar beet
egg plant sunflower
eucalyptus tobacco
fir tomato
guava viburnum
hibiscus walnut
hops zucchini

5. Oomycete Genome Comparisons
• P. sojae vs P.ramorum vs P. infestans
– ~9,800 orthologs
– 45-55% of genome orthologous
– 25-45% in recognizable gene families
– ~10% unique
• H. arabidopsidis
– ~4400 orthologs
– most gene families smaller
– some genes missing
• zoospore function
• inorganic sulfur and nitrogen assimilation

6. Conserved gene order within the Peronosporales
Hyaloperonospora
arabidopsidis
scaffolds 9; 126; 7; 47
Baxter et al 2010
Phytophthora
infestans
supercontig1.1
Haas et al 2009
Phytophthora
ramorum
scaffold_1
Tyler et al 2006
Pythium ultimum
scf1117875581354
Levesque et al 2010
PHRINGE analysis: Jeff Boore

7. Effector genes are associated with repeat rich
regions in oomycete genomes
Haas et al (2009) Nature 461(7262): 393-399

8. Protein toxin genes have expanded subsequent to speciation
the NPP1 family Credit: Mark Gijzen
Necrosis = death: P. sojae
effect of P.sojae NIP P. ramorum
Qutob et al Plant J. 32, 361, 2002

9. Rapidly diverging RXLR superfamily in Oomycetes
median 27aa 14aa 126aa
range 10-67aa 7-55aa 28-835aa
Signal Peptide RXLR dEER
P. sojae ~400
P. ramorum ~370
P. infestans ~550
H. arabidopsidis ~130
Includes 16/17
cloned oomycete
avirulence genes
PsAvr1a, PsAvr1b,
PsAvr1k, PsAvr3a,
PsAvr3b, PsAvr3c,
PsAvr4/6, PsAvr5
PiAvr1, PiAvr2,
PiAvr3a, PiAvr4,
PiAvrPlb1/ipiO1,
PiAvrPlb2,
HaAtr1, HaAtr13
Jiang et al PNAS HaAtr5
105(12), 4874-4879 (2008)

10. Data, data, everywhere but ...
is it knowledge?
 Even today the ability to generate high throughput
sequencing and other “omic” data is outstripping the ability
to transform the data into knowledge
 Automated data processing pipelines are not a substitute
for human insight

11. Integration of Oomycete & Fungal Database
Resources
VMD
vmd.vbi.vt.edu
FungiDB
www.FungiDB.org
DOE JGI Mycocosm
http://genome.jgi-
psf.org/programs/fung
i/index.jsf

12. PERL and a Pipetman
Life in a data-rich environment
Every experimental biologist needs to be a computational
biologist too
 Theory  Experiment
 Modeling  Simulation