tyler presentation
DESCRIPTION
Oomycetes OverviewTRANSCRIPT
• National Science Foundation
– Research Coordination Networks in Biology
– Oomycete Genomics Research Collaboration Network
– 2007-2012
• USDA CSREES and NSF
– Microbial Genome Sequencing Program
– Finishing the P. sojae Genome Sequence
– 2007-2011
• USDA NIFA
– Oomycete Coordinated Agricultural Project
– Integrated management of oomycete diseases of soybean and other crop plants
– 2011-2016
Funding Acknowledgements
Oomycete Genomics, Past, Present and Future
Brett Tyler
Virginia Bioinformatics InstituteVirginia Polytechnic Institute and State University
Past
Oomycete Genome ComparisonsOomycete 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
• 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
Conserved gene order within the Peronosporales
Phytophthora infestanssupercontig1.1Haas et al 2009
Pythium ultimum
scf1117875581354
Levesque et al 2010
Hyaloperonospora arabidopsidisscaffolds 9; 126; 7; 47Baxter et al 2010
Phytophthora ramorumscaffold_1Tyler et al 2006
PHRINGE analysis: Jeff Boore
Effector genes are associated with repeat rich regions in oomycete genomes
Haas et al (2009) Nature 461(7262): 393-399
Necrosis = death: effect of P.sojae NIPNecrosis = death: effect of P.sojae NIP
Protein toxin genes have expanded subsequent to speciation the NPP1 family Credit: Mark Gijzen
Qutob et al Plant J. 32, 361, 2002
P. sojaeP. ramorum
Rapidly diverging RXLR superfamily in Oomycetes
P. sojae ~400P. ramorum ~370P. infestans ~550H. arabidopsidis ~130
Signal Peptide RXLR dEER
27aa10-67aa
14aa7-55aa
126aa28-835aa
medianrange
Includes 16/17 cloned oomycete avirulence genesPsAvr1a, PsAvr1b, PsAvr1k, PsAvr3a,PsAvr3b, PsAvr3c, PsAvr4/6, PsAvr5PiAvr1, PiAvr2,PiAvr3a, PiAvr4, PiAvrPlb1/ipiO1, PiAvrPlb2, HaAtr1, HaAtr13HaAtr5Jiang et al PNAS
105(12), 4874-4879 (2008)
Present
• New 25X BAC library with 150 kb inserts; fully end-sequenced• New assembly using Arachne and BAC data• 454 sequencing of three more genotypes of P. sojae• Genetic mapping with SNPs to join physical and genetic maps• Automated gap-filling and sequence improvement• Targeted finishing of BACs using primer walking and transposon
insertion• 100m ABI Solid™ RNA sequence tags (75 nt)• New annotation utilizing RNA seq data and manual annotations
from v1.0• 8000 new genes
• Upgrades to VMD browser• Undergraduate bioinformatics network
Finishing of the P. sojae Genome Sequence
Hudson Alpha Institute; DOE JGI; Texas A&M; VBI
Future
• Sanger sequencing with Megabace
– $1000/1 Mb raw sequence– 1 machine -> 1 Mb/day– 800-900 bp per read
• 454 Life Sciences Pyrosequencing
– $30/1 Mb raw sequence– 1 machine (Titanium) -> 1 Gb/day– 400-500 bp per read
• Illumina bead sequencing; ABI SOLID
– $0.11/1 Mb raw sequence– 1 machine -> 25 Gb/day (HiSeq 2000)– 50-100 bp per read
• Pacific Biosciences
– upcoming single molecule sequencing technology– $0.03/1 Mb raw sequence? ($1000 human genome)– 1000-10,000 bp/ read?
Rapid improvement in sequencing capacity
P. sojae 9x2003 $1.34mP. sojae 9x2003 $1.34m
P. sojae 9x2009 $25,000P. sojae 9x2009 $25,000
alfalfaalmondappleapricotavocadoazaleabananabean (Phaseolus)blackberryblueberryBrassicacabbagecacaocanolacantaloupecarnationcauliflowercedarchestnutchickpeacitrusclovercoconutcoffeecottoncowpeacranberrycucurbitsdate palm egg planteucalyptusfirguavahibiscushops
larchmacadamiamelonmustardoakoil palmpapayapassionfruitpea (Pisum)peachpearpecanpepperperiwinklepinepineapplepistachioplumpomegranatepotatopumpkinraspberryrhododendronsafflowersesamesoybeansquashstrawberrysugar beetsunflowertobaccotomatoviburnumwalnutzucchini
PhytophthoraGenome
Sequencing
Some Phytophthora hosts
Sequenced
In progress
> 120 destructive pathogen species
Integration of Oomycete & Fungal Database Resources
FungiDB
www.FungiDB.org
DOE JGI Mycocosm
http://genome.jgi-psf.org/programs/fungi/index.jsf
VMD
vmd.vbi.vt.edu