1. Genomics of Microbial Eukaryotes Igor Grigoriev Fungal Genomics Program Head US DOE Joint Genome Institute, Walnut Creek, CA

2. 2 Outline  Eukaryotic Genome Annotation  Fungal Genomics Program  MycoCosm

3. 3 Are you in the right room? genome.jgi.doe.gov IMG MycoCosm 100+ annotated eukaryotic genomes

4. 4 Started with Human Genome Project

5. 5 Protein-based methods build CDS exons around known protein alignments. (Fgenesh, GeneWise) GenBank protein Transcript-based methods map or assemble transcripts on the genome, including UTRs (EST_map, Combest) EST contig Predict model Ab initio methods use knowledge of known genes’ structures to predict start, stop, and splice sites in CDS only. (Fgenesh+, GeneMark) Train on known genes ATG TGA GT AG exonsintrons 5’UTR 3’UTR Promoter PolyA Gene model Eukaryotic Gene Prediction

6. 6 Predicted protein Protein Annotation Higher order assignments: Gene Ontology terms EC numbers --> KEGG pathways Gene families, with and without other species Possible orthologs (in nr, SwissProt, KEGG, KOG) Possible paralog (Blastp+MCL) Domain (InterPro, tmhmm) Signal peptide (signalP)

7. 7 EST Support is Critical for Eukaryotes Sanger454Illumina 5531 34 EST profile CombEST gene models

8. 8 Best Models FGENESH Representative set GENEWISE EXTERNAL MODELS  Multiple gene predictors offer several different gene models at each gene locus;  A single best model from each locus is automatically selected based on homology and EST support;  These compose a non-redundant (or Filtered) gene set for further analysis  This set is further improved during community-driven manual curation

9. 9 Genomic assembly and EST contigs Annotation Pipeline Gene predictions Protein annotations Transcript + protein maps Repeat mask Manual curation Bring it all together Analysis Gene families Gene expression Phylogenomics Proteomics Protein targeting etc Annotation

10. 10 Many Genes of Eco-responsive Daphnia pulex First crustacean, aquatic animal sequenced, new model organism 30,940 predicted D.pulex genes in ~200Mb genome 85% supported by 1+ lines of evidence Colbourne et al, Science, 2011

11. 11 Half of Daphnia Genes have no Homologs With Evgeny Zdobnov’s group (Univ. Genève) * Of 716 highly conserved single copy orthologs, Daphnia is missing only two

12. 12 Outline Eukaryotic Genome Annotation  Fungal Genomics Program  MycoCosm

13. 13 Fungal Genomics for Energy and Environment Grow Grow Degrade Degrade Lignocellulose degradation Plant symbionts and pathogens Sugar Fermentation Ferment Ferment Bio-refinery GOAL: Scale up sequencing and analysis of fungal diversity for DOE science and applications

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15. 15 Plant feedstock health Symbiosis Plant Pathogenicity Biocontrol Biorefinery fungi Lignocellulose degradation Sugar fermentation Industrial organisms Fungal diversity Phylogentic Ecologic Genomic Encyclopedia of Fungi Launched www.jgi.doe.gov/fungi 100+ fungal genomes 600+ registered users 5000+ visitors/month

16. 16 Distinct Mechanisms of Cellulose Degradation White rot P.chrysosporium Cellobiohydrolase II GH6(CBH50) Cellobiohydrolase I GH7 (CBH58,62) Endoglucanases GH5-CBM1,GH12 GH3  -glucosidase Cellulose No cellulose binding domain CBM1 in brown rot! Fe 2+ + H 2 O 2 Fe 3+ + HO - + HO. Fe 3+ Glucose Copper radical oxidases Glucose oxidases Iron reductase Brown rot Postia placenta Martinez et al, PNAS 2009

17. 17 Diverse Basidiomycota FGP09 pilots Basidio jam (Mar 2010) 3 CSP11 proposals Basidio jam (Mar 2011)

18. 18 Future Grand Challenges Fungal isolates & groups Systems of interacting organisms Systems in wild MODELING FUNCTION SEQUENCE 1.1000 fungal genomes sampling fungal diversity 2.Model fungi sampling 100s of conditions 3.Fungal ecosystems:  Bioenergy crops symbionts & pathogens  Biorefinery  Fungal metagenomes

19. 19 Leadership in Sequencing Fungi

20. 20 Annotation and Analysis Tools Automated Annotation Pipeline Genomics Analysis Platform Genome Centric Comparative Genomics Community Resource Integrated data User tools Training

21. 21 Genome-Centric View Comparative View www.jgi.doe.gov/fungi

22. 22 Genome-Centric View Focus: functional genomics, user data deposition and curation

23. 23 New Comparative View

24. 24 Community Building Tools Jamborees: Genome analysis for publications MycoCosm Tutorials: On-line video, MGM, workshops w/ large meetings (Asilomar, JGI Users, MSA) Preparation for CSP: Large meetings and focused groups

25. 25 Summary Eukaryotic Annotation Recipe: Combined gene predictors, experimental data, and community annotation Fungal Genomics Program: Scaled-up sequencing & comparative analysis of fungi relevant for energy & environment (jgi.doe.gov/fungi)

26. 26 Outline Eukaryotic Genome Annotation Fungal Genomics Program  MycoCosm