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Phytophthora Small RNA Database: Visualization of Small RNAs Using a Genome Viewer

Phytophthora Small RNA Database: Visualization of Small RNAs Using a Genome Viewer . Deepthika Ennamuri Mentor: Dr. Niklaus J. Grünwald REU Summer 2011 Internship Horticultural Crops Research Laboratory. USDA - National Institute of Food and Agriculture Grant. $9 million grant

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Phytophthora Small RNA Database: Visualization of Small RNAs Using a Genome Viewer

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  1. PhytophthoraSmall RNA Database: Visualization of Small RNAs Using a Genome Viewer Deepthika Ennamuri Mentor: Dr. Niklaus J. Grünwald REU Summer 2011 InternshipHorticultural Crops Research Laboratory

  2. USDA - National Institute of Food and Agriculture Grant • $9 million grant • Develop methods to manage Late Blight Disease http://www.csrees.usda.gov

  3. Phytophthora • Genus of water molds • Resemble fungi in growth habits • More closely related to Brown Algae • Resistant to most fungicides • 100+ species have been discovered • Some species can attack up to hundreds of different plant host species http://www.cdfa.ca.gov

  4. Phytophthora • Cause root, fruit and stem rots on numerous species of plants • First show symptoms of drought and starvation • Affected plants become weaker and susceptible to attack by other pathogens or conditions http://www.nasa.gov/vision/earth/environment/invasive_agreement.html

  5. Phytophthorainfestans • Caused Irish potato famine • Causes Late Blight Disease • Destroys potato and tomato plants • Costs $6.7 billion dollars annually • Thrives in rainy and humid environments http://usablight.org/?q=node/18

  6. Phytophthorasojae • Affects soybeans • Costs $1-2 billion dollars annually • Present in almost all soybean producing nations • Can infect seeds,  seedlings, and mature plants http://www.plantpath.wisc.edu/soyhealth/prr.htm

  7. Small RNAs • Major role in regulating gene expression in eukaryotes • Interfere with gene expression • Degradation and repression of transcripts • Small pieces of RNA bind to target mRNA and block its translation

  8. Significance • Understand: • The mechanisms these pathogens use to break down plants’ defenses • Use P. sojaeas a model to understand Phytophthoragene regulation • Aim: • Organize current small RNA information into a working online database

  9. Summer 2011 Project • Develop a publicly accessible Phytophthora small RNA database • Identify target genes • miRNA sequence, gene ID, gene function • Perl (programming language) • Reannotate current P. sojaegenome sequences • MAKER – annotation tool • Rxlr and Crinkler genes – gene families involved in infection

  10. Materials • Perl • A dynamic programming language • MAKER • Genome annotation tool • Generic Genome Browser v2.4 (GBrowse) • Genome viewing tool • Ability to display different types of data

  11. GBrowse

  12. Identifying miRNAs • Identify potential miRNA loci • Capture FASTA sequence for the region

  13. Create foldback structure to determine if region contains miRNA

  14. Reannotating the P. sojaeGenome

  15. Results • http://phytophthora-smallrna-db.cgrb.oregonstate.edu/

  16. miRNA

  17. Artificial miRNA

  18. Acknowledgments • Dr. Niklaus Grünwald • Stephanie Bollmann • Chris Sullivan • Josh Cuperus • Howard Hughes Medical Institute • Dr. Kevin Ahern • USDA – NIFA • US NSF - REU

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