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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 <ivgrigoriev@lbl.gov>. 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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  1. Genomics of Microbial Eukaryotes Igor Grigoriev, Fungal Genomics Program Head US DOE Joint Genome Institute, Walnut Creek, CA <ivgrigoriev@lbl.gov>

  2. Large and Complex Eukaryotes

  3. Outline • Eukaryotic Genome Annotation • Fungal Genomics Program • MycoCosm

  4. Started with Human Genome Project

  5. IMG MycoCosm 150+ annotated eukaryotic genomes genome.jgi.doe.gov

  6. 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

  7. 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

  8. 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

  9. Combine Gene Predictors for Better Quality Heterobasidion annosum v1.0

  10. Re-annotation Using Comparative Genomics Asaf Salamov

  11. 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

  12. Validation with Transcriptomics models Old Sanger Days ESTs Transformation of EST sequencing Sanger 454 Illumina Processing RNA-Seq with CombEST 5531 34 EST profile

  13. Validation with Proteomics Wright et al, BMC Genomics (2009)

  14. Gene Cluster Analysis Comparative analysis

  15. Genome Portal Framework

  16. 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

  17. 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)

  18. Outline • Eukaryotic Genome Annotation • Fungal Genomics Program • MycoCosm

  19. 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

  20. 758 fungal projects GOLD (October 2011)

  21. 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

  22. Comparative View Genome-Centric View http://jgi.doe.gov/fungi 100+ fungal genomes 5000+ visitors/month

  23. Comparative Genome Analysis

  24. 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.

  25. Strategy: Fungal Systems Lichen: alga+fungus T.terrestris ECM:plant+fungus Forest soil metagenomes S.commune Complex environments Simple systems Model fungi

  26. Model Mushroom Development Ohm et al, 2010 Gene knock-outs WTD S.commune Modeling regulatory cascades <Transcriptomics> FUNCTION MODEL SEQUENCE

  27. 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)

  28. Enjoy Algae as well! http://genome.jgi.doe.gov/Algae

  29. Acknowledgements JGI Staff Our Users

  30. Outline • Eukaryotic Genome Annotation • Fungal Genomics Program • MycoCosm

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