Genomics of microbial eukaryotes
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Genomics of Microbial Eukaryotes. Igor Grigoriev, Fungal Genomics Program Head US DOE Joint Genome Institute, Walnut Creek, CA <[email protected]>. Large and Complex Eukaryotes. Outline. Eukaryotic Genome Annotation Fungal Genomics Program MycoCosm. Started with Human Genome Project.

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Genomics of Microbial Eukaryotes

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Genomics of microbial eukaryotes

Genomics of Microbial Eukaryotes

Igor Grigoriev,

Fungal Genomics Program Head

US DOE Joint Genome Institute, Walnut Creek, CA

<[email protected]>


Large and complex eukaryotes

Large and Complex Eukaryotes


Outline

Outline

  • Eukaryotic Genome Annotation

  • Fungal Genomics Program

  • MycoCosm


Started with human genome project

Started with Human Genome Project


Genomics of microbial eukaryotes

IMG

MycoCosm

150+ annotated eukaryotic genomes

genome.jgi.doe.gov


Annotation pipeline

Annotation Pipeline

Gene families

Gene expression

Phylogenomics

Proteomics

Protein targeting

etc

Analysis

Genomic assembly and ESTs

Repeat masking

Reference data mapping

Annotation Pipeline

Gene predictions

Protein annotations

Validations

Manual curation (optional)

Annotation


Eukaryotic gene prediction

Eukaryotic Gene Prediction

Promoter

TGA

ATG

PolyA

GT

AG

Gene model

3’UTR

5’UTR

exons

introns

Train on known genes

Ab initio methods

use knowledge of known genes’ structures to predict start, stop, and splice sites in CDS only. (Fgenesh+, GeneMark)

Transcript-based methods

map or assemble transcripts on the genome, including UTRs (EST_map, Combest)

EST contig

Predict model

Protein-based methods

build CDS exons around known protein alignments.

(Fgenesh, GeneWise)

GenBank protein

Predict model


More gene prediction

More Gene Prediction

Predicted model

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

  • ESTEXT

ESTs

Extended model

5’UTR

3’UTR

  • Detect orthologs with poor alignments and refine with synteny based methods

  • FGENESH2

ATG

TGA

Genome A

Genome B

TGA

ATG

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

Representative set

FGENESH

GENEWISE

EXTERNAL MODELS


Combine gene predictors for better quality

Combine Gene Predictors for Better Quality

Heterobasidion annosum v1.0


Re annotation using comparative genomics

Re-annotation Using Comparative Genomics

Asaf Salamov


Protein annotation

Protein Annotation

Signal peptide

(signalP)

Domain

(InterPro, tmhmm)

Possible orthologs

(in nr, SwissProt, KEGG, KOG)

Possible paralog

(Blastp+MCL)

Higher order assignments:

Gene Ontology terms

EC numbers --> KEGG pathways

Gene families, with and without other species

Predicted protein


Validation with transcriptomics

Validation with Transcriptomics

models

Old Sanger Days

ESTs

Transformation of EST sequencing

Sanger

454

Illumina

Processing RNA-Seq with CombEST

5531

34

EST profile


Validation with proteomics

Validation with Proteomics

Wright et al, BMC Genomics (2009)


Gene cluster analysis

Gene Cluster Analysis

Comparative analysis


Genome portal framework

Genome Portal Framework


Genomics of microbial eukaryotes

Many Genes of Eco-responsive Daphnia pulex

First crustacean, aquatic animal sequenced, new model organism30,940 predicted D.pulex genes in ~200Mb genome85% supported by1+ lines of evidence

Colbourne et al, Science, 2011


Genomics of microbial eukaryotes

Half of Daphnia Genes: no Homologs, Experessed Under Environmental Stress

* Of 716 highly conserved single copy orthologs, Daphnia is missing only two

Colbourne et al, 2011

With Evgeny Zdobnov’s group (Univ. Genève)


Outline1

Outline

  • Eukaryotic Genome Annotation

  • Fungal Genomics Program

  • MycoCosm


Fungal genomics for energy environment

Fungal Genomics for Energy & Environment

Bio-refinery

Plant symbiontsand pathogens

Lignocellulose degradation

SugarFermentation

Degrade

Ferment

Grow

GOAL: Scale up sequencing and analysis of fungal diversity for DOE science and applications


Genomics of microbial eukaryotes

758 fungal projects

GOLD (October 2011)


Genomics of microbial eukaryotes

Genomic Encyclopedia of Fungi

  • Chapter 1: Plant health

    • Symbiosis

    • Plant Pathogenicity

    • Biocontrol

  • Chapter 2: Biorefinery

    • Lignocellulose degradation

    • Sugar fermentation

    • Industrial organisms

  • Chapter 3: Diversity

    • Phylogentics

    • Ecology


Genomics of microbial eukaryotes

Comparative View

Genome-Centric View

http://jgi.doe.gov/fungi

100+ fungal genomes

5000+ visitors/month


Comparative genome analysis

Comparative Genome Analysis


Strategy 1000 fungal genomes

Strategy:1000 Fungal Genomes

Goal:Sequencing 1000 fungal genomes from across the Fungal Tree of Life will provide references for research on plant-microbe interactions and environmental metagenomics.


Strategy fungal systems

Strategy: Fungal Systems

Lichen: alga+fungus

T.terrestris

ECM:plant+fungus

Forest soil metagenomes

S.commune

Complex environments

Simple systems

Model fungi


Model mushroom development

Model Mushroom Development

Ohm et al, 2010

Gene knock-outs

WTD

S.commune

Modeling regulatory cascades

<Transcriptomics>

FUNCTION

MODEL

SEQUENCE


Summary

Summary

Eukaryotic Annotation Recipe:

Combine gene predictors, experimental data, and community expertise

Fungal Genomics: we aim to

scale-up sequencing & comparative analysis of fungi relevant for energy & environment (jgi.doe.gov/fungi)


Enjoy algae as well

Enjoy Algae as well!

http://genome.jgi.doe.gov/Algae


Acknowledgements

Acknowledgements

JGI Staff

Our Users


Outline2

Outline

  • Eukaryotic Genome Annotation

  • Fungal Genomics Program

  • MycoCosm


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