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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

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


Usda national institute of food and agriculture grant
USDA - National Institute of Food and Agriculture Grant

  • $9 million grant

  • Develop methods to manage Late Blight Disease

http://www.csrees.usda.gov


Phytophthora
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


Phytophthora1
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


Phytophthora infestans
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


Phytophthora sojae
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


Small rnas
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


Significance
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


Summer 2011 project
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


Materials
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



Identifying mirnas
Identifying miRNAs

  • Identify potential miRNA loci

  • Capture FASTA sequence for the region


Phytophthora small rna database visualization of small rnas using a genome viewer

  • Create foldback structure to determine if region contains miRNA


Reannotating the p sojae genome
Reannotating the P. sojaeGenome


Results
Results

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




Acknowledgments
Acknowledgments

  • Dr. Niklaus Grünwald

    • Stephanie Bollmann

    • Chris Sullivan

    • Josh Cuperus

  • Howard Hughes Medical Institute

    • Dr. Kevin Ahern

  • USDA – NIFA

  • US NSF - REU