The Eukaryote Tree of Life: a Genomics Perspective

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The Eukaryote Tree of Lifea Genomics Perspective
Sandie Baldauf Univ of York slb14_at_york.ac.uk
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Eukaryotic Cells Have 1-4 Genomes ( plasmids?)
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Origin and Evolution of Mitochondrion
v Eukaryote alpha-proteobacterium
(endosymbiosis) - early in euk evolution, before
LCA
v modern mitochondria - mitogenome 12-120
genes - nuclear genome 400 genes (40 aP, 200
novel)

• Anaerobic parasites (e.g., Entamoeba,
  Trichomonas, Giardia)
• - reduced mito-like organelles (hydrogenosome,
  mitosome)
• - no mitogenome

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Origin and Evolution of Eukaryotic Photosynthesis

• origin of eukaryotic photosynthesis
  cynobacterium -gt eukaryote
• primary endosymbiosis happened once (maybe)

• followed by much lateral transfer, secondary
  endosymbiosis
• many attempts (past and present), major
  success chl ac algae

Chlorarachniophytes Cryptophytes
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Genome Origins
v Mitochondrial genomes - 12-120 genes,
??-proteobacterial origin - also introns,
intervening DNA, bits of chloroplast DNA

• Chloroplast genomes 150-200 genes,
  cyanobacterial origin
• sometimes accompanying nucleomorph primary
  eukaryote host

v Nuclear genome - mixed origin - archael (esp.
info processing) - novel (eukaryotic
origin) - ?-proteobacterial from
mitochondrion - cyanobacterial from
chloroplast - other bacterial (some LGT)
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The Tree of Life2006
Baldauf, et al., in Assembling the Tree of Life,
2004
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Major Groups of Eukaryotes
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1. OpisthokontsAnimals Fungi

• many trees
• all multigene trees

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Protistan Allies of Animals and Fungi
Steenkamp, Wright Baldauf, submitted)
Steenkamp, Wright, Baldauf, Mol. Biol. Evol., 2006
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OpisthokontsGenomics
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2. Amoebozoa
- amoebas with lobose pseudopodia
- amitochondriate amoeboflagellates

• parasites

• social amoebas
• (slime molds)

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Amoebozoan Amoebas
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Mycetozoa 1Myxomycetes/Plasmodial Slime Molds
(Giant Amoebas)
up to 1 ft diameter, no internal cell walls
10,000 synchronously dividing nuclei
mobile (1 cm/hour)
ornate (acellular) fruiting bodies
photographs by Michel Poulain
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Mycetozoa 2 Social AmoebasDictyostelidae
(Cellular Slime Molds)

• solitary amoebae -gt
• 10,000 cell aggregates

? model system cell-cell signaling -
(cAMP) simplified development
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SSU rDNA Phylogeny of Dictyostelia
(Schaap et al., Science in press)
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Amoebozoan Genomics
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3. Rhizaria (Testate Amoebas)
Rampant transient symbioses, 1 group true
algae Chlorarachniophytes
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Rhizarian Genomes
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4. Archaeplastida (formerly Plantae)

• red algae
• green algae
• (incl land plants)
• glaucocystophytes
• origin of eukaryotic
• photosynthesis
• (primary endosymbiosis)

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Archaeplastida Genomics
land plants
Coleochaete
Charales
Zygnemetales
Klebsormidiales
Chlorophytes
Chlorokybales
prasinophyte (Mantoniella?)
Chlorophyta
Ulvophyta
Trebouxiophyta
prasinophytes
Floridiophytes
Hildenbrandia
Bangiales (Porphyra)
Rhodophytes
Porphyridiales 1 (Stylonema)
Compsopogonales
Porphyridiales 2 (Dixoniella, Rhodella)
Cyanidiales
Glaucophytes
Glaucophyta
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5,6 Chromalveolates
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Alveolates

• Apicomplexa (Sporozoa)
• - malaria 1 protistan killer
• of humans (and other vertebrates)
• - secondary endosymbiont (apicomplast
  chloroplast derived organelle)

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Chromalveolates II Stramenopiles
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ChromalveolatesCryptophytes and Haptophytes
Haptophytes (coccolithophorids) - calcium
carbonate scales - massive blooms -gt
chalk deposits - most abundamt photosynthetic
euk cells on planet

• Cryptophytes
• enslved red algal symbiont
• remnant primary host nucleus
• (nucleomorph)

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ChromalveolateGenomics
Apicomplexa
Dinoflagellates
Marine Group I
Alveolates
Marine Group II (Syndineales)
Colpodella
Perkinsus
Ciliates
chl ac algae (x14)
diatoms
Oomycetes (water molds)
Bicosoecids
Stramenopiles
Labyrinthulids
Actinophryid (heliozoa)
Opalinids
Haptophyta
Cryptophyta
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7. Excavates I Discicristates
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8. Amitochondriate Excavates

• . Parasites or symbionts, anaerobes, simplified
  cells
• possibly near root of tree

? phylogeny poorly understood - large complex
group of truly strange things
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Excavate Genomics
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Acknowledgements
Eukaryotic phonotosynthesis - Johanna Fehling
Eukaryote Tree - Andrew Roger Ford Doolittle
(Dalhousie), Ingrid Wenk-Siefert (Zurich)
Opisthokont Protists - Emma Steenkamp Jane
Wright (York/Pretoria) Choanoflaellates - Martin
Carr (York), Ruhanna Hassan Barry Leadbeater
(Bham)
Dictyostelidae - Michaela Nelson, Barrie Elgie,
Lavinia Paternoster, Sobbia Saleem, Samantha
Wilkinson Pauline Schaap Elisa Alvarez-Curtos
(Dundee) Thomas Winkler Rupert Mutzel
(Berlin) James Cavcender (Ohioi), Hiromitcus
Hagewara (Japan)
Myxogastriae - Anne-Marie Fiore, Cedric Berney,
Jan Pawlowski (Univ Geneva)
Amoeobozoa - Jan Pawlowski (Univ Geneva), Tom
Cavalier-Smith (Oxford)
Funding - BBSRC, Royal Society, Wolfson Foundation
Pictures - Paddy Patterson (Microscope project)
_at_ Woods Hole www.mbl.edu/microscope