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Eukaryotic Genome Annotation

Eukaryotic Genome Annotation. Asaf Salamov, Fungal Genomics Program US DOE Joint Genome Institute, Walnut Creek, CA. Started with Human Genome Project. IMG. MycoCosm. 150+ annotated eukaryotic genomes. genome.jgi.doe.gov. Annotation Pipeline. Gene families Gene expression Phylogenomics

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Eukaryotic Genome Annotation

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  1. Eukaryotic Genome Annotation Asaf Salamov, Fungal Genomics Program US DOE Joint Genome Institute, Walnut Creek, CA

  2. Started with Human Genome Project

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

  4. 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

  5. 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

  6. 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

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

  8. Re-annotation Using Comparative Genomics

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

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

  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. Gene Cluster Analysis Comparative analysis

  13. Genome Portal Framework

  14. Daphnia pulex – Environmental Model First crustacean, aquatic animal sequenced New model organism Compact genome (~200Mb) Largest gene count (~31,000) Unknown genes most responsive to environmental changes Colbourne et al, Science, Feb 4, 2011 14

  15. 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)

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