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Seminar at SIU, Medellín Friday August 28th, 2009

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  1. 1. Origin and Evolution of Early Eukaryotes James McInerney, National University of Ireland Maynooth, August 25th, 2009,
  2. 2. And the LORD God made all kinds of trees grow out of the ground--trees that were pleasing to the eye and good for food. In the middle of the garden were the tree of life and the tree of the knowledge of good and evil. Genesis 2:9
  3. 3. Hypothesis Implied Relationship s Phylogenetic signals expected in genomic analys e s Tree of lifea Archaea and Eukaryota Eukaryotic genes should show 3 are sister groups. monophyletic domains or Eukaryota Archaebacteria . Eukaryota- Eukaryota is the first Most eukaryotic genes should not have a firstb diverging domain, while prokaryotic homologue. Others should Eubacteria and Archaea show 3 monophyletic domains or are sister groups. Eukaryota with Archaebacteria . Eocytec Eukaryota is the sister Eukaryotic genes with Crenarchaeota . group of Crenarchaeota . Phagotrophyd Eukaryota and Archaea Eukaryotic genes with Archaebacteria, are sister groups. This and these two with Actinobacteria. group stemmed from Actinobacteria . Serial Symbiosis of a Eukaryotic genes with Thermoplasma, endosymbiosise Thermoplasma-like spirochetes or -Proteobacteria . archaeon and a spirochete (Eubacteria). Mitochondria probably via symbiosis with an - proteobacterium. Syntrophy-1f Eukaryota originated Eukaryotic genes with methanogenic through the symbiosis of a Archaea (or within Euryarchaeota), - or methanogen and a - -Proteobacteria. proteobacterium. Hydrogen Eukaryota originated Eukaryotic genes with methanogenic Hypothesisg through the symbiosis of a Archaea (or within Euryarchaeota) or - methanogen and an - Proteobacteria . proteobacterium (the mitochondrion) . Syntrophy-2h Eukaryota originated Eukaryotic genes with Thermoplasmatales through the symbiosis of a (or within Euryarchaeota) or - sulfur-methabolising Proteobacteria . Thermoplasmatales-like euryarchaeote and an - proteobacterium (the mitochondrion) . Ring of lifei Eukaryota originated Eukaryotic genes with Crenarchaeota or through the symbiosis of a -Proteobacteria. Crenarchaeota and an - proteobacterium.
  4. 4. Mitochondrion origins
  5. 5. Rhodospirillum rubrum • Rickettsia prowazekii
  6. 6. Comparisons of the same bacterial species E. coli K12 E. Coli 0157:H7
  7. 7. Horizontal gene transfer does occur between species McInerney, J.O., Cotton, J.A. and Pisani, D. (2008) The Prokaryotic Tree of Life: Past, Present...and Future? Trends in Ecology and Evolution 23 (5) 276-281
  8. 8. Doubts concerning a universal tree …most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. …If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Ford Doolittle Phylogenetic classification and the universal tree. Doolittle WF. Science. 1999 Nov 19;286(5444):1443
  9. 9. The importance of congruence • “The importance, for classification, of trifling characters, mainly depends on their being correlated with several other characters of more or less importance. The value indeed of an aggregate of characters is very evident ...a classification founded on any single character, however important that may be, has always failed.” • Charles Darwin • Origin of Species, Ch. 13
  10. 10. Source Trees …. x1 x2 x3 x4 x... xn Candidate Supertree Score = ∑xn
  11. 11. Supertree Source tree
  12. 12. Alpha-proteobacteria Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2006). Genome Phylogenies Indicate a Meaningful α-Proteobacterial Phylogeny and Support A Grouping of the Mitochondria With the Rickettsiales. Molecular Biology and Evolution 23: 74-85.
  13. 13. The mitochondrion is descended from a common ancestor with the Rickettsiales.
  14. 14. Pisani, D., Cotton, J.A. and McInerney, J.O. (2007). Supertrees Disentangle the Chimerical Origin of Eukaryote Genomes. Molecular Biology and Evolution. 24(8):1752–1760.
  15. 15. Archaeb acteria Bacteria
  16. 16. Modularity
  17. 17. Protocol • All Saccharomyces cerevisiae proteins subjected to homology search against Caenorhabditis elegans, Arabidopsis thaliana, Schizosaccharomyces pombe, Neurospora crassa, Ashbya gossypii, Trypanosoma cruzi. • Multiple alignment of resulting significant hits and profile search against prokaryotic genomes (197 bacterial, 22 archaebacterial). • Two datasets used: – Phylogeny-dependent – Phylogeny independent
  18. 18. Overview • 2,460 out of 6,704 genes have prokaryotic homologs. • 1,980 genes have a eubacterial best hit, 480 archaebacterial. • 952 genes have only eubacterial homologs, 216 only archaebacterial.
  19. 19. So there is a larger role for eubacterial homologs •Right?
  20. 20. Importance? • Which is more important…. – An informational or an operational gene? – A highly-expressed gene or a lowly- expressed gene? – A gene that is central to metabolism or one that is peripheral? – A gene that is lethal upon knockout or one that is not?
  21. 21. Odds ratio • We describe associations between factors using the odds ratio. • e.g., the odds of being archaebacterial for informational genes is calculated as the probability of an informational gene having an archaebacterial homolog, divided by the probability of the gene having a eubacterial homolog. • We can similarly calculate the odds of being archaebacterial for operational genes, and the odds ratio is the ratio of these two odds.
  22. 22. Confirmation of informational bias • We confirm a significant bias towards archaebacterial homology for genes with informational functions (odds ratio (or)=2.37; 95% confidence interval (ci)=1.59-3.52), although genes with archaebacterial homologs are found across most gene ontology biological processes.
  23. 23. Link between lethality and informational genes • Lethal genes are almost three times as likely to have archaebacterial homologs than bacterial ones (or=2.96; 2.32-3.77). • Informational genes are significantly more likely to be lethal than operational genes (or=2.98; 2.03-4.40).
  24. 24. Link between lethality and Archaebacterial homology • Lethality of archaebacterial genes is almost identical across the two categories (for informational genes, or=2.01; 0.92-4.41; for operational genes, or=1.89; 1.43-2.47)
  25. 25. DATATYPE Bact Arch All p-value L phase, number of SAGE tags sequenced 1.76 (1.43,2.17) 3.42 (2.15,5.16) 1.96 (1.74,2.21) 0.0034 S phase, number of SAGE tags sequenced 1.93 (1.59,2.33) 2.97 (1.94,4.35) 2.05 (1.82,2.30) 0.0395 G2/M phase boundary, number of SAGE tags 1.55 (1.27,1.88) 2.99 (1.97,4.39) 2.04 (1.81,2.28) 0.0028 sequenced Closeness Centrality in interaction network 0.314 0.324 0.316 < 0.0001 (0.312,0.316) (0.321,0.327) (0.315,0.317) Degree in interaction network 15.91 20.90 18.02 < 0.0001 (15.20,16.62) (19.33,22.48) (17.60,18.48) Number of homologs in yeast genome 13.13 8.02 (6.89,9.22) 7.58 (7.14,8.04) 1 (12.09,14.16) P-values are bootstrap probabilities for the mean of the statistic in archaebacteria being less than or equal to the mean in eubacteria, based on 10,000 replicates.
  26. 26. Threonine and lysine metabolism
  27. 27. Pentose phosphate pathway
  28. 28. Arginine metabolism
  29. 29. • Eukaryote “Tree” – Davide Pisani – James Cotton – Angela McCann • Prokaryotic “Tree” – Chris Creevey – David Fitzpatrick – Mary O’Connell – Melissa Pentony – Simon Travers – Rhoda Kinsella – Gayle Philip – Jennifer Commins – Thomas Keane • Supertree Theory – Dr. Mark Wilkinson, Natural History Museum. • Irish Centre for High End Computing • NUIM HPC • Funding: – Marie Curie – SFI – IRCSET.