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Bioinformatics and Evolutionary Genomics The tree of life / HGT , origin of eukaryotes

Bioinformatics and Evolutionary Genomics The tree of life / HGT , origin of eukaryotes. LUCA. “three kingdoms”. How to root the tree of life? 1: Find paralogs that duplicated before the LUCA. 6 found so far.

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Bioinformatics and Evolutionary Genomics The tree of life / HGT , origin of eukaryotes

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  1. Bioinformatics and Evolutionary GenomicsThe tree of life / HGT , origin of eukaryotes

  2. LUCA “three kingdoms”

  3. How to root the tree of life?1: Find paralogs that duplicated before the LUCA 6 found so far

  4. How to root the tree of life? 2: Make a tree of paralogs that duplicated before the LUCA Griblado 1998 J Mol Evol Griblado 1998 J Mol Evol

  5. How ta make a tree of life?Issue: Horizontal Gene Transfer (HGT) • As opposed to normal vertical inheritance • Inheritance from somewhere else than parents • AKA lateral gene transfer

  6. Bs1 Mg1 Ec1 Rp1 Ct1 Af1 HGT

  7. Bs1 Mg1 Ec1 Rp1 Ct1 Af1 HGT

  8. Bs2 Mg2 Bs1 Mg1 Ec1 Rp1 Ct1 Af1 HGT

  9. Bs2 Mg2 Ec1 Rp1 Ct1 Af1 HGT

  10. HGT: frequently observed when many genome sequences became available

  11. HGT & Tree of Life (ToL) b

  12. Transition prokaryotes to eukaryotes: big transition • The prekaryote • No more intermediates • How to look before the event horizon?

  13. Endo symbiosis of alpha proteo-bacteria gave rise to mitochondria • Mitochondrial DNA in the mitochondria • Hydrogenosomes shown to be derived from mitochondria • Many proteins active in present-day mitochondria are coded for by proteins of eukaryotic invention, archaeal descent • Many proteins of alpha-protein ancestor active in in other parts of the cell B

  14. rRNA tree Mitochondria have their own mini genome 16S Ribosomal RNA

  15. Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny A B Eukaryotic + alpha-proteobacteria in the same branch Alpha-proteobacterial proteins with the rest of the bacteria and archaea

  16. GENOMES SELECTION OF HOMOLOGS, (Smith&Waterman) LIST ALIGNMENTS AND TREE (Clustalx, Kimura+Dayhoff) PHYLOME Detecting eukaryotic genes of alpha-proteobacterial ancestry GENOME 6 alpha-proteobacteria (22 500 genes) 6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea TREE SCANNING

  17. Proto-mitochondrial metabolism: - Catabolism of fatty acids, glycerol and amino acids.- Some pathways are not mitochondrial. non-mitoch.. mitochondrial not in yeast/human

  18. The majority of the proto-mitochondrial proteome is not mitochondrial (anymore) 566 Gabaldon & Huynen Science 2003 alpha-prot. Yeast mitochondrial proteome: Eric Schon, Methods Cell Biol 2001 (manually curated) 35 303 59 293 10 Huh et al., Nature 2003 (green fluorescent genomics) 527 755 Human mitochondrial proteome: Eric Schon, Methods Cell Biol 2001 113 508

  19. proteins ~65% of the alpha-proteobacteria derived set is not mitochondrial. loss re-targeting Ancestor ~16% of the mitochondrial yeast proteins are of alpha-proteobacterial origin. gain t From endosymbiont to organell, not only loss and gain of proteins but also “retargeting”: Modern mitochondria Gabaldon and Huynen, Science 2004

  20. “When” did the mitochondria invade the eukaryotes? • Genes from alpha-proteobacterial descent present in genomes in mitochondria-less organisms (cf. toni) • All eukaryotes have or had a mitochondria/alpha proteobacterial symbiont • It thus happened before the last common ancestor of all eukaryotes • But then still “when”? (b)

  21. what about all other cellular innovations that set eukaryotes apart from prokaryotes?

  22. the prekaryote-LECA transition Makarova NAR 2005

  23. Duplication more prevalent in pre-eukaryotes that in archaea or bacteria Makarova NAR 2005

  24. duplications: e.g. small GTPases

  25. Thus all these duplications & endosymbios order? • Unknown but all before eluca • According to the theory of endocytosis as a late thing for the prekaryote, after many of the eukaryotic inventions: to be tested involvement of genes of alpha-prot origin in crucial (cellular) euk processes? (nuclear import)

  26. Eukaryotic tree of life? • The divisions: • Ophistokonts (animals, fungi, microsporidia) • Amoebozoa (Dicty) • Chromalveolata Paramecium, Plasmodium but also diatoms • Archaeplastida • Excavata • Rhizaria • Historically: crown-group eukaryotes vs protists • What is a complete genome; draft genomes

  27. Animals • Most primitive: sponges • Quite a number of genome sequences (of dubious completeness)

  28. Fungi • Many complete genomes • Broad, Genolevures • Microsporidium (E. cuniculi) • Mushrooms are Basidomyctes • Together with animals: ophistokonts

  29. Amoebozoa • Few genomes • Entamoeba histolytica • Dictyostelium discoideum

  30. Archaeplastida • Second bacterial endosymbiosis event: cyanobacteria • Green algae, red algae, plants • ~5 genomes

  31. Chromalveoates • Secondary endosymbios: plastids • Very different species • (diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, dinoflagelates) • Quite some genomes (~10) B

  32. Excavata • Weird parasites (Giardia, Trypanosome, Leismania) • But also: Naegleria gruberi: amoeboflagelate

  33. Rhizaria • Amoeboids + amoeboflagellates • produce shells which make up the vast majority of protozoan fossils. • No genomes (yet)

  34. How are eukaryotes related ??? • Historically: crown-group eykaryotes vs protists but now molecular evidence • Two hypothesis: • In or just after excavata • Inbetween ophistokonts/amoebozoa vs the rest (unikont vs bikont), myosins • Rhizaria? • phagotrophic origin of eukaryotes: an amoebe with flagella? b

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