Genome Evolution

1. Genome Evolution Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca

2. Causes of genomic evolution • Variation in genome size • Variation in genomic GC% • Variation in gene content • Variation between strands • Variation in DNA methylation and gene regulation

3. Variation in genome size C-value paradox: - in certain cases, lack of correlation between morphological complexity and genome size “[For] some commonly cited extreme values for amoebae... considerable uncertainty about the accuracy of these measurements and the ploidy level of the species...” Gregory Nature Rev. Genet. 6:699, 2005 Table 8.3 & Alberts Fig.1.38

4. Gene fraction vs. genome size Function of non-genic DNA in eukaryotes? Composition of human genome Gregory Nature Rev. Genet. 6:699, 2005 Fig. 8.15

5. Variation in prokaryotic gene content Fig. 8.1

6. New genes and new gene interactions Hartwell Fig. 21.11

7. chr I chr II chr III chr IV chr V Duplicated sequences in yeast genome whole genome duplication ~ 100 Mya? Text Fig. 8.7 In Arabidopsis, ~ 60-70% genome present in duplicate copy Many multi-gene families ( ~ 65% genes are duplicated, and ~ 40% of these families have > 5 members) Nature 408:796, 2000

8. Lateral gene transfer “Bacterial speciation is likely to be driven by a high rate of horizontal transfer, which introduces novel genes, confers beneficial phenotypic capabilities, and permits the rapid exploitation of competitive environments”. Ochman Nature 405: 299, 2000

9. Molecular archaeology of the E.coli genome Transposition events (IS elements) Horizontal gene transfer Lawrence & Ochman PNAS 95:9413, 1998

10. Genome reduction in obligate parasites Rickettsia prowazekii causative agent of typhus intracellular parasite a-proteobacteria – respiratory chain very similar to mitochondrial one Andersson Nature 396: 133, 1998

11. Bacterial genomic GC and codon usage Fig.8.26 Fig. 8.29 consequences for codon usage patterns?

12. GC% in bacteriophage and their hosts Natural selection Natural selection AT-biased mutation

13. Empirical Data dsDNA Phage Non-dsDNA phage

14. Variation between strands in bacteria Bacterial genomes have bias for G on leading strand of bidirectional replication fork - replication error differences between leading and lagging DNA strands Marin, A. and Xia, X. 2008. GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand-bias. Journal of Theoretical Biology 253(3):508-513 Fig. 8.27

15. “Experimental evolution” in vivo Comparison of positions of orthologous genes in Mycoplasma & Haemophilus Fig.8.22 Papdopoulos, PNAS 96:3807, 1999

16. Search for a “minimal” genome E. coli Search for “minimal” bacterial genome Haemophilus influenzae Mycoplasma genitalium Fig. 8.1 Search for “signature proteins” distinctive for 3 “domains of life” eg. archaeal-specific (no detectable homologues in other lineages) = 350 Woese PNAS 97:3302, 2000 eg. eukaryotic-specific = 915 (or315if include Giardia - parasite with reduced gene set) Hartman PNAS 99:1420, 2002