Tyler future of genomics thurs 0920

Oomycete Genomics, Past, Present and Future Brett Tyler Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University

Systems Biology of Host-Pathogen Interactions A single genetic network encompasses host and pathogen

Host-pathogen interactions are influenced by higher scale network connections to... … microbial communities

Estuarine Ecosystem. www.centralcoastbc.com … and macroecosystems

Integration and Complexity ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

A Wholistic View of Biological Systems ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Oomycete Genome Sequencing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],completed or near completed

Oomycete Genome Sequencing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],nearing completion or just completed

Oomycete Genome Sequencing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Funded and in progress

Albugo candida Lagenidium giganteum Hyaloperonospora arabidopsidis Bremia lactucae Phytophthora parasitica Peronospora tabacina Phytophthora sojae* *** Peronosporomycetidae Phytophthora capsici Phytophthora ramorum Plasmopara viticola Peronosporales Aphanomyces astaci Pythium ultimum** Phytophthora phaseoli Phytophthora ipomoae Phytophthora andina Phytophthora mirabilis Phytophthora infestans* ** Saprolegniomycetidae Pythiales/Lagenidiales Saprolegnia parasitica Saprolegnia diclina Aphanomyces euteiches high quality assembly short read survey genome funding sought Oomycete Genome Sequencing Summary ESTs * *** strains sequenced

Sequencing of P. sojae genotypes P7064 P7074 P7076 P6497

Oomycete RXLR Effector Proteins ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Signal Peptide RXLR dEER 27aa 10-67aa 14aa 7-55aa 126aa 28-835aa median range RXLR+GFP

How RXLR effectors enter plant cells pathogen (fungus or oomycete) host plant cell P endocytosis Avr1b lipid rafts P P P P P PI-3-P binding protein Avr1b + PEPP1 Avr1b + 1,3 IP2 P P Inositol-1,3- diphosphate

Data collection in the coming decade ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Rapid improvement in sequencing capacity ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],P. sojae 9x 2003 $1.34m P. sojae 9x 2009 $25,000

[object Object],[object Object],[object Object],[object Object],[object Object],Data collection over time and space Concentrations and locations of nucleic acids, proteins and metabolites

Sequence analysis will move from snapshots to movies ,[object Object],[object Object],[object Object]

The Data Challenge ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Data, data, everywhere but ... ,[object Object],[object Object],[object Object]

PERL and a Pipetman Life in a data-rich environment Every experimental biologist needs to be a computational biologist too ,[object Object],[object Object],[object Object],[object Object]

New paradigm in undergraduate research VBI, Virginia Tech Year-round mentoring Summer Training Workshops Undergraduate consortium in oomycete bioinformatics Lafayette College Manuel Ospina-Giraldo 3 undergraduates Bowling Green State U Paul Morris; Karen Sirum 5 undergraduates College of Wooster, OH Bill Morgan funded by NSF/USDA microbial sequencing program Franklin & Marshall College Jaime Blair Nova Southeastern College Aurelian Tartar

Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Tyler future of genomics thurs 0920

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Tyler future of genomics thurs 0920