Poxviruses and Adaptive Genome Evolution

1. Poxviruses and Adaptive Genome Evolution Aoife McLysaght Dept. of Genetics Trinity College Dublin

2. Genome Evolution • Evolution of genome arrangement • Evolution of genome content • .

3. Genome Evolution • Evolution of genome arrangement • Gene order changes • Inversions, translocations • Evolution of genome content • .

4. Genome Evolution • Evolution of genome arrangement • Gene order changes • Inversions, translocations • Evolution of genome content • Gene gain (sequence divergence, duplication, recombination, horizontal transfer) • Gene loss (deletion) • .

5. Genome Evolution • Evolution of genome arrangement • Gene order changes • Inversions, translocations • Evolution of genome content • Gene gain (sequence divergence, duplication, recombination, horizontal transfer) • Gene loss (deletion) • One or more genes per event

6. Genome Evolution • Translate knowledge from sequenced or model genomes to organism of interest • Positional cloning of genes • Use probes designed in one genome to detect a target in another genome • Improve model parameters for phylogenetic inference from genome arrangement

7. Genome Structure • Not just a bag of genes • Genome organisation contains information • Order of Hox genes corresponds to spatial pattern of gene expression • Clustering of housekeeping genes • By observation of ‘allowed’ changes gain understanding of genomic constraints and plasticity

8. Multiple Genome Comparison • Greater power to detect change • Precision • Can infer lineage in which change occurred • Detect direction and rate of change • More genomes also increase computational burden

9. Pox virus genomes • 20 completely sequenced genomes • 150-300kb containing ~200 genes

10. Poxviruses • Double-stranded DNA viruses, no RNA stage • Replicate in the host cytoplasm • Entomopox – insect infecting • Chordopox – vertebrate infecting • Orthopox – subset of chordopox which includes smallpox (variola) and vaccinia

11. Questions: • How are these genomes arranged? • How has genome content changed? • Is the rate of change constant?

12. Questions: • How are these genomes arranged? • How has genome content changed? • Is the rate of change constant? • Can we detect adaptive genome evolution?

13. Orthologue detection Significant sequence similarity • How significant? over a long stretch of the protein • How long?

15. Complete linkage • Single-link clustering • Our method

16. Complete linkage C A E B D

17. Single-link clustering C A E G F B D

18. C E A J F D B I C G E H D B

19. Orthologues • 4042 total proteins • 3384 proteins classified into 875 groups • 813 complete linkage • 521 groups of 1 member • 150 groups of 2 members • 204 ≥ 3 members

20. Conserved gene order and spacing

21. Poxvirus Phylogeny 34 orthologues present in all genomes

22. Poxvirus Phylogeny 34 orthologues present in all genomes

23. Orthopox phylogeny 92 orthologues present in all orthopox genomes

24. Counting gene gain and loss • Examine phylogenetic spread of a group of orthologues • Assign gene gain and loss events to branches in the phylogeny

25. Phylogenomic Approach

26. Infer gene gain along the branch to the most recent common ancestor

27. Infer gene loss parsimoniously

28. Numbers of gain/loss events

29. Numbers of gain/loss events

30. Rate of Gene Gain • Tested for uniform rate of gene acquisition • Assume a molecular clock

31. Rate of Gene Gain • Tested for uniform rate of gene acquisition • Assume a molecular clock • Are gene acquisition events distributed randomly throughout the tree?

32. Rate of Gene Gain • Tested for uniform rate of gene acquisition • Assume a molecular clock • Are gene acquisition events distributed randomly throughout the tree? • Simulations

33. Significant deficit Significant excess

34. Increased Gene Gain in the Orthopox Lineage • Slower rate of amino acid substitution within this clade (leading to abberantly short branch lengths) • Takezaki relative rate test • Branch lengths from synonymous distances

35. Increased Gene Gain in the Orthopox Lineage • Slower rate of amino acid substitution within this clade (leading to abberantly short branch lengths) • Takezaki relative rate test • Branch lengths from synonymous distances • Increased rate of gene gain • Increased selection for the retention of gained genes

36. Sources of Gene Acquisition • Extensive sequence divergence • Recombination • Horizontal transfer

37. Horizontal Transfer • AMV-EPB_034 – inhibitor of apoptosis from Amsacta moorei entomopoxvirus (AMV-EPB) • GenBank sequence – inhibitor of apoptosis from Bombyx mori (silkworm) BLAST e-value 9e-81 • Amsacta moorei entomopoxvirus infects Amsacta moorei (Red Hairy Caterpillar) • Bombyx and Amsacta both OrderLepidoptera

38. Horizontal Transfer • AMV-EPB_034 – inhibitor of apoptosis from Amsacta moorei entomopoxvirus (AMV-EPB) • GenBank sequence – inhibitor of apoptosis from Bombyx mori (silkworm) BLAST e-value 9e-81 • Amsacta moorei entomopoxvirus infects Amsacta moorei (Red Hairy Caterpillar) • Bombyx and Amsacta both OrderLepidoptera • 62% of best non-viral GenBank hits are from same taxonomic Class as viral host

39. Gene loss modelling • Events are not independent • Depend on previous (in time) gain and loss events of the gene family • Requires a probabilistic model?

40. Gene loss events

41. Adaptive Evolution • Selection for diversification • Positive selection • Characteristic of host-parasite co-evolution

42. Standard Genetic Code

43. Detection of Positive Selection • Two classes of DNA substitutions • Synonymous (DNA change without amino acid change) • Nonsynonymous (DNA change causing amino acid change) • Neutral – equal frequencies • Conservative selection – fewer nonsynonymous substitutions • Positive selection – more nonsynonymous substitutions

44. Detection of Positive Selection • Two classes of DNA substitutions • Synonymous (DNA change without amino acid change) • Nonsynonymous (DNA change causing amino acid change) • Neutral – equal frequencies • Conservative selection – fewer nonsynonymous substitutions • Positive selection – more nonsynonymous substitutions

45. Detection of Positive Selection • Two classes of DNA substitutions • Synonymous (DNA change without amino acid change) • Nonsynonymous (DNA change causing amino acid change) • Neutral – equal frequencies • Conservative selection – fewer nonsynonymous substitutions • Positive selection – more nonsynonymous substitutions

46. Detection of Positive Selection • Two classes of DNA substitutions • Synonymous (DNA change without amino acid change) • Nonsynonymous (DNA change causing amino acid change) • Neutral – equal frequencies • Conservative selection – fewer nonsynonymous substitutions • Positive selection – more nonsynonymous substitutions

47. Detection of Positive Selection • 204 groups of orthologues • Maximum liklihood test for positive selection (PAML) • Significantly higher frequency of nonsynonymous substitutions

48. Positive Selection on Pox Genes • Detected positive selection on 26 genes • Examples: • Membrane glycoprotein • Haemagluttinin • Immunoglobulin domain protein

49. Positive Selection on Pox Genes • 13 genes are unique to orthopox clade • Significantly more than expected (P < 0.05) • Disproportionate frequency of positive selection on genes gained within the orthopox lineage

50. Adaptive Genome Evolution? • Association of positive selection on protein sequences and increased rate of gene acquisition