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. GrünwaldREU Summer 2011 InternshipHorticultural Crops Research

Laboratory

USDA - National Institute of Food and Agriculture Grant$9 million grantDevelop

methods to manage Late Blight Disease

http://www.csrees.usda.gov

Phytophthora Genus of water moldsResemble 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

Phytophthora Cause root, fruit and stem rots on

numerous species of plantsFirst show symptoms of drought and

starvationAffected plants become weaker and susceptible to attack by other pathogens or conditions  

http://www.nasa.gov/vision/earth/environment/invasive_agreement.html

Phytophthora infestans Caused Irish potato famine Causes Late Blight Disease

◦Destroys potato and tomato plantsCosts $6.7 billion dollars annuallyThrives in rainy and humid environments

http://usablight.org/?q=node/18

Phytophthora sojae Affects soybeansCosts $1-2 billion

dollars annuallyPresent in almost

all soybean producing nations

Can infect seeds,  seedlings, and mature plants http://www.plantpath.wisc.edu/soyhealth/prr.htm

Small RNAsMajor 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 Understand:

◦The mechanisms these pathogens use to break down plants’ defenses

◦Use P. sojae as a model to understand Phytophthora gene regulation

Aim:◦Organize current small RNA

information into a working online database

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. sojae genome

sequences MAKER – annotation tool Rxlr and Crinkler genes – gene families

involved in infection

MaterialsPerl

◦A dynamic programming language MAKER

◦Genome annotation tool Generic Genome Browser v2.4

(GBrowse)◦Genome viewing tool ◦Ability to display different types of

data

GBrowse

Identifying miRNAsIdentify potential miRNA lociCapture FASTA sequence for the region

Create foldback structure to determine if region contains miRNA

Reannotating the P. sojae Genome Properly format P. sojae and P. infestans FASTA files

Run FASTA files through MAKER

MAKER outputs GFF3 files

Format P. infestans and P.sojae GFF3 files

Upload P. sojae and P. infestans small RNA GFF3 files to database

Results http://phytophthora-smallrna-db.

cgrb.oregonstate.edu/

miRNA

Artificial miRNA

Acknowledgments Dr. Niklaus Grünwald

◦ Stephanie Bollmann ◦ Chris Sullivan◦ Josh Cuperus

Howard Hughes Medical Institute◦ Dr. Kevin Ahern

USDA – NIFAUS NSF - REU