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Poxvirus Genomics & Bioinformatics “How to manage and analyze poxvirus genomes…… and still have time for a beer”

Poxvirus Genomics & Bioinformatics “How to manage and analyze poxvirus genomes…… and still have time for a beer”. Dr. Chris Upton University of Victoria British Columbia. Projects. 1) Virulence proteins (NSERC). 2) Bioinformatics (NIH and PENCE) The Poxvirus Bioinformatics Resource.

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Poxvirus Genomics & Bioinformatics “How to manage and analyze poxvirus genomes…… and still have time for a beer”

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  1. Poxvirus Genomics & Bioinformatics “How to manage and analyze poxvirus genomes…… and still have time for a beer” Dr. Chris Upton University of Victoria British Columbia

  2. Projects 1) Virulence proteins (NSERC) 2) Bioinformatics (NIH and PENCE) The Poxvirus Bioinformatics Resource 3) Protein structures (PENCE) Poxviruses - introduction

  3. Poxviruses Genus Species Disease/Applications Orthopoxvirus variola smallpox vaccinia vaccine for smallpox expression vector cancer vaccines ectromelia mousepox monkeypox potential “new smallpox” Molluscipoxvirus molluscum contagiosum human pathogen Leporipoxvirus myxoma myxomatosis Avipoxvirus fowlpox non-replicating vaccines canarypox

  4. Genome Structure TIR TIR non-essential non-essential essential replication transcription virion virulence virulence genome 150 - 300 kb 150 + genes

  5. CompletedGenomes (26+) Variola major virus Variola minor virus Vaccinia virus Monkeypox virus (2) Camelpox virus Ectromelia virus Rabbitpox virus Rabbit fibroma virus Myxoma virus strain Lausanne Fowlpox virus Molluscum contagiosum virus subtype 1 Yaba virus Swinepox virus Lumpy skin disease virus Sheeppox Amsacta moorei entomopoxvirus Melanoplus sanguinipes entomopoxvirus

  6. Virulence Genes TNF binding proteins Interferon-gamma binding protein Chemokine binding protein IL-1 binding protein IL-18 binding protein Interferon-alpha/betabinding proteins Growth factor-like proteins RING finger protein (apoptosis) Serpins (>3; ICE inhibitor) Schlafen homolog

  7. Virulence Summary Large number of virulence genes Different genes important in different viruses Expression levels are likely as important as gene complement

  8. Genome sequencing Software development Data management Gene prediction Accurate annotation Genome evolution 2) Bioinformatics The Poxvirus Bioinformatics Resource

  9. Frame 1 a) 1 b) 1 2 3 4 5 6 c) Identification of fragmented genes & Non-coding ORFs

  10. Genome Sequencing Ectromelia virus Rabbitpox Monkeypox (2 strains)

  11. Software Development(user-friendly tools) Base-by-Base Poxvirus Ortholog Clusters (POCs) Viral Genome Organizer (VGO) JDotter

  12. Poxvirus Orthologous Clusters - POCs Database containing all complete poxvirus genomes proteins, DNA, pI, nucleotide composition, codon use, aa composition, promoter type Genes grouped into families after BLAST comparisons Allows manual family assignment and annotation Families can be aligned & edited with JalView Works with bacterial genomes & spliced genes

  13. POCs Results - Identification of 300 gene families (orthologs) - Minimum essential genome: 49 genes in all poxviruses (26) (9 “unknown”) + 41 genes in all Chordopoxviruses (24) (7 “unknown”) - Corrected 12 GenBank gene entries - Resequenced 10 “missing genes” from Vaccinia (TT)

  14. Conservation of genes amongst poxvirus

  15. Viral Genome Organizer - VGO Manipulates complete genomes Pre-process BlastP and PSI-Blast (NCBI NR) searches Provides graphical interface to: genome organization protein and DNA sequences BLAST search results POCs database Links to: local software WWW-based programs

  16. Mview alignment of BlastP results

  17. For comparative studies: VGO works with multiple genomes

  18. JDotter Java interface to Dotter Plot storage & management

  19. Base-by-Base Alignment editor for complete genomes Describe differences between 2 genomes Nucleotide accuracy - mapped to genes substitutions, insertions, deletions, inversions, transpositions

  20. Collaborators University of Victoria Dr. Rachel Roper St. Louis University School of Medicine Dr. Mark Buller University of Alabama, Birmingham Dr. Elliot Lefkowitz www.poxvirus.org Acknowledgments The Lab Gui-Yun Li Melissa Da Silva Christine Butler-Cole Maria Danila Arwen Hunter Monika Fazekas Angelika Ehlers Ryan Brodie Fei Zhang

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