MycoCosm & JGI Oomycete Genomics Tools

Andrea AertsEukaryotic Genomics Program

US DOE Joint Genome Institute, Walnut Creek, CA

<alaerts@lbl.gov>

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US DOE Joint Genome Institute

• Opened in 1999• 250+ people• Budget: ~$70M• Location: Walnut Creek, CA

www.jgi.doe.gov

bioenergy, carbon cycling & biogeochemistry

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Are you in the right room?

genome.jgi-psf.org

IMG

MycoCosm

70+ annotated eukaryotic genomes

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Outline

Eukaryotic Genome Annotation

MycoCosm

Manual Curation

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Started with Human Genome Project

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Automated Annotation Pipeline

Quality Control

Gene Prediction

Data Mapping

Repeat Masking

Annotation

Genome assembly and ESTs

Repeat Library

Training predictors

External gene sets

Optional Inputs Automated Pipeline Staged Portal Release

External data sets

Manual curation

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Eukaryotic Gene Prediction

Ab initio gene prediction is based on knowledge of general features of gene structure trained on a set of known genes.FGENESH

GENEMARK

Homology methods build exons around regions of homology and ensure gene structure features.

Homolog

Predicted model

Known genes are mapped onto genomic sequence

mRNA

Known gene

ATG TGA

GT AG

exons introns5’UTR3’UTR

Promoter PolyA

Gene model

GENEWISEFGENESH+,

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More Prediction Methods

Use ESTs/cDNAs to extend, correct or predict gene models

• ESTEXT

Predicted model

ESTs

Extended model

5’UTR 3’UTR

ATG TGA

ATG TGADetect orthologs with poor alignments and refine with synteny based methods • FGENESH2

Genome A

Genome B

FGENESH

Representative set

GENEWISE

EXTERNAL MODELS

Non-redundant gene set is built from “the best” models from each locus according to homology and ESTs, followed by manual curation

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Outline

Eukaryotic Genome Annotation

MycoCosm

Manual Curation

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Ly

Genome-Centric View

Comparative View

www.jgi.doe.gov/fungi

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Genome-Centric View

Focus: functional genomics, user data deposition and curation

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New Comparative View

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Community Building Tools

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Asilomar, Pacific Grove, CA (Mar 15-20): Mar 15: Dothideomycetes jamboree Mar 17: JGI Workshop (Fungi & CSP) Mar 18: Fungal Tools (MycoCosm)Walnut Creek, CA (Mar 21-24): Mar 21: Basidiomycetes jamboree Mar 22: MycoCosm tutorial

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Oomycetes at JGI

• Phytophthora ramorum• Phytophthora sojae

• improved assembly • released “internally” in April 2011

• Phytophthora capsici• Hybrid Sanger/454 assembly • Public release November 2010

• Phytophthora cinnamomi• Currently in sequencing

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Outline

Eukaryotic Genome Annotation

MycoCosm

Manual Curation

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Manual Curation Tools

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Manual Curation Workflow

1. Find a gene2. Validate gene structure3. Choose the best model4. Fix the structure or report the problems5. Annotate it!

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1. Find a Gene

• Search using keywords• Browse KEGG/GO/KOG lists• Blat/Blast your sequence against genome,

transcripts, proteins• Search by ID (Simple search for model name,

protein id, gi number)

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2. Validate Gene Structure

Using GenomeBrowser, check:ESTs; Genome conservation; Homology;Other evidence (eg, proteomics, tiling arrays)

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2. Validate Gene Structure, cont

Using Protein Pages, check:Alignments with homologs; Domains

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2. Validate Gene Structure, cont

Using Cluster Details pages, compare:

sizes and domain composition of orthologs

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4. Fix Gene Structure

• If the best not good enough report that it requires editing (AnnotationPage), or fix it (TrackEditor) and then promote it (AnnotationPage)

• If there is no model, create it (TrackEditor) and then promote it (AnnotationPage)

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5. Annotate Gene

Using AnnotationPage, assign:• Gene name/symbol (optional)• Defline (mandatory, will go to GenBank)• Description (optional)• Notes (‘No issues’ if the model is good)• Disposition (‘Catalog’ or ‘Delete’)

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Hands-on demo

• http://genome.jgi-psf.org/Oomycetes/• Login

• oomyceteworkshop@gmail.com• workshop234