Bioinformatics and Evolutionary Bioinformatics and Evolutionary GenomicsGenomics

The tree of life / HGT , origin of The tree of life / HGT , origin of eukaryoteseukaryotes

Bioinformatics and Evolutionary Bioinformatics and Evolutionary GenomicsGenomics

The tree of life / HGT , origin of The tree of life / HGT , origin of eukaryoteseukaryotes

LUCA

“three kingdoms”

How to root the tree of life?How to root the tree of life?1: Find paralogs that duplicated before the 1: Find paralogs that duplicated before the

LUCALUCA

How to root the tree of life?How to root the tree of life?1: Find paralogs that duplicated before the 1: Find paralogs that duplicated before the

LUCALUCA

6 found so far

How to root the tree of life? 2: Make a tree of How to root the tree of life? 2: Make a tree of paralogs that duplicated before the LUCAparalogs that duplicated before the LUCA

How to root the tree of life? 2: Make a tree of How to root the tree of life? 2: Make a tree of paralogs that duplicated before the LUCAparalogs that duplicated before the LUCA

Griblado 1998 J Mol Evol

Griblado 1998 J Mol Evol

How ta make a tree of life?How ta make a tree of life?Issue: Horizontal Gene Transfer (HGT)Issue: Horizontal Gene Transfer (HGT)

How ta make a tree of life?How ta make a tree of life?Issue: Horizontal Gene Transfer (HGT)Issue: Horizontal Gene Transfer (HGT)

• As opposed to As opposed to normal vertical normal vertical inheritanceinheritance

• Inheritance from Inheritance from somewhere else somewhere else than parentsthan parents

• AKA lateral gene AKA lateral gene transfertransfer

• As opposed to As opposed to normal vertical normal vertical inheritanceinheritance

• Inheritance from Inheritance from somewhere else somewhere else than parentsthan parents

• AKA lateral gene AKA lateral gene transfertransfer

HGTHGTHGTHGT

Bs1Bs1 Mg1Mg1Ec1Ec1Ct1Ct1

Rp1Rp1

Af1Af1

HGTHGTHGTHGT

Bs1Bs1 Mg1Mg1Ec1Ec1Ct1Ct1

Rp1Rp1

Af1Af1

HGTHGTHGTHGT

Bs2Bs2 Mg2Mg2

Bs1Bs1 Mg1Mg1Ec1Ec1Ct1Ct1

Rp1Rp1

Af1Af1

HGTHGTHGTHGT

Bs2Bs2 Mg2Mg2

Ec1Ec1Ct1Ct1

Rp1Rp1

Af1Af1

HGT: frequently observed when many HGT: frequently observed when many genome sequences became availablegenome sequences became availableHGT: frequently observed when many HGT: frequently observed when many genome sequences became availablegenome sequences became available

HGT & Tree of Life (ToL)HGT & Tree of Life (ToL)HGT & Tree of Life (ToL)HGT & Tree of Life (ToL)

b

Transition prokaryotes to eukaryotes: big Transition prokaryotes to eukaryotes: big transitiontransition

Transition prokaryotes to eukaryotes: big Transition prokaryotes to eukaryotes: big transitiontransition

• The prekaryoteThe prekaryote

• No more intermediatesNo more intermediates

• How to look before the event horizon?How to look before the event horizon?

• The prekaryoteThe prekaryote

• No more intermediatesNo more intermediates

• How to look before the event horizon?How to look before the event horizon?

Endo symbiosis of alpha proteo-bacteria gave Endo symbiosis of alpha proteo-bacteria gave rise to mitochondriarise to mitochondria

Endo symbiosis of alpha proteo-bacteria gave Endo symbiosis of alpha proteo-bacteria gave rise to mitochondriarise to mitochondria

• Mitochondrial DNA in the mitochondriaMitochondrial DNA in the mitochondria

• Hydrogenosomes shown to be derived from Hydrogenosomes shown to be derived from mitochondriamitochondria

• Many proteins active in present-day mitochondria Many proteins active in present-day mitochondria are coded for by proteins of eukaryotic invention, are coded for by proteins of eukaryotic invention, archaeal descentarchaeal descent

• Many proteins of alpha-protein ancestor active in Many proteins of alpha-protein ancestor active in in other parts of the cellin other parts of the cell

• Mitochondrial DNA in the mitochondriaMitochondrial DNA in the mitochondria

• Hydrogenosomes shown to be derived from Hydrogenosomes shown to be derived from mitochondriamitochondria

• Many proteins active in present-day mitochondria Many proteins active in present-day mitochondria are coded for by proteins of eukaryotic invention, are coded for by proteins of eukaryotic invention, archaeal descentarchaeal descent

• Many proteins of alpha-protein ancestor active in Many proteins of alpha-protein ancestor active in in other parts of the cellin other parts of the cell

B

rRNA tree rRNA tree rRNA tree rRNA tree

16S Ribosomal RNA

Mitochondria have their own mini genome

Alpha-proteobacterial proteins with the rest of the bacteria and archaea

Eukaryotic + alpha-proteobacteria in the same branch

Identifying Identifying eukaryoticeukaryotic proteins with proteins with an an alpha-proteobacterialalpha-proteobacterial origin based origin based

on their phylogenyon their phylogeny

Identifying Identifying eukaryoticeukaryotic proteins with proteins with an an alpha-proteobacterialalpha-proteobacterial origin based origin based

on their phylogenyon their phylogeny

PHYLOME

SELECTION OF HOMOLOGS,(Smith&Waterman)

ALIGNMENTS AND TREE(Clustalx, Kimura+Dayhoff)

GENOME

GENOMES

TREE SCANNING

LIST

Detecting eukaryotic genes of alpha-proteobacterial ancestryDetecting eukaryotic genes of alpha-proteobacterial ancestry

6 alpha-proteobacteria9 eukaryotes56 Bacteria+Archaea

6 alpha-proteobacteria (22 500 genes)

- Catabolism of fatty acids, glycerol and amino acids.- Catabolism of fatty acids, glycerol and amino acids.- Some pathways are - Some pathways are not mitochondrialnot mitochondrial..

Proto-mitochondrial metabolism:Proto-mitochondrial metabolism:

non-mitoch..

mitochondrial

not in yeast/human

Eric Schon, Methods Cell Biol 2001(manually curated)

Huh et al., Nature 2003Huh et al., Nature 2003(green fluorescent genomics)(green fluorescent genomics)

566

527

303

Gabaldon & HuynenScience 2003alpha-prot.

10

59

35

293

Yeast mitochondrial proteome:Yeast mitochondrial proteome:

Human mitochondrial proteome:Human mitochondrial proteome:

Eric Schon, Methods Cell Biol 2001

755

508

The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)

113

t

proteinsloss

gain

re-targeting

AncestorModern mitochondria

From endosymbiont to organell, not only From endosymbiont to organell, not only loss and gain of proteins but also loss and gain of proteins but also “retargeting”:“retargeting”:

~16% of the mitochondrial yeast proteins are of alpha-proteobacterial origin.

~65% of the alpha-proteobacteria derived set is not mitochondrial.

Gabaldon and Huynen, Science 2004

““When” did the mitochondria invade the When” did the mitochondria invade the eukaryotes?eukaryotes?

““When” did the mitochondria invade the When” did the mitochondria invade the eukaryotes?eukaryotes?

• Genes from alpha-proteobacterial descent Genes from alpha-proteobacterial descent present in genomes in mitochondria-less present in genomes in mitochondria-less organisms (cf. toni)organisms (cf. toni)

• All eukaryotes have or had a mitochondria/alpha All eukaryotes have or had a mitochondria/alpha proteobacterial symbiontproteobacterial symbiont

• It thus happened before the last common It thus happened before the last common ancestor of all eukaryotesancestor of all eukaryotes

• But then still “when”? (b)But then still “when”? (b)

• Genes from alpha-proteobacterial descent Genes from alpha-proteobacterial descent present in genomes in mitochondria-less present in genomes in mitochondria-less organisms (cf. toni)organisms (cf. toni)

• All eukaryotes have or had a mitochondria/alpha All eukaryotes have or had a mitochondria/alpha proteobacterial symbiontproteobacterial symbiont

• It thus happened before the last common It thus happened before the last common ancestor of all eukaryotesancestor of all eukaryotes

• But then still “when”? (b)But then still “when”? (b)

what about all other cellular innovations what about all other cellular innovations that set eukaryotes apart from that set eukaryotes apart from

prokaryotes?prokaryotes?

what about all other cellular innovations what about all other cellular innovations that set eukaryotes apart from that set eukaryotes apart from

prokaryotes?prokaryotes?

the prekaryote-LECA transitionthe prekaryote-LECA transitionthe prekaryote-LECA transitionthe prekaryote-LECA transition

Makarova NAR 2005

Duplication more prevalent in pre-Duplication more prevalent in pre-eukaryotes that in archaea or bacteriaeukaryotes that in archaea or bacteria

Duplication more prevalent in pre-Duplication more prevalent in pre-eukaryotes that in archaea or bacteriaeukaryotes that in archaea or bacteria

Makarova NAR 2005

duplications: e.g. duplications: e.g. small GTPasessmall GTPases

duplications: e.g. duplications: e.g. small GTPasessmall GTPases

Thus all these duplications & endosymbios Thus all these duplications & endosymbios order?order?

Thus all these duplications & endosymbios Thus all these duplications & endosymbios order?order?

• Unknown but all before elucaUnknown but all before eluca

• According to the theory of endocytosis as a late According to the theory of endocytosis as a late thing for the prekaryote, after many of the thing for the prekaryote, after many of the eukaryotic inventions: to be tested involvement of eukaryotic inventions: to be tested involvement of genes of alpha-prot origin in crucial (cellular) euk genes of alpha-prot origin in crucial (cellular) euk processes? processes?

(nuclear import)(nuclear import)

• Unknown but all before elucaUnknown but all before eluca

• According to the theory of endocytosis as a late According to the theory of endocytosis as a late thing for the prekaryote, after many of the thing for the prekaryote, after many of the eukaryotic inventions: to be tested involvement of eukaryotic inventions: to be tested involvement of genes of alpha-prot origin in crucial (cellular) euk genes of alpha-prot origin in crucial (cellular) euk processes? processes?

(nuclear import)(nuclear import)

Eukaryotic tree of life?Eukaryotic tree of life?Eukaryotic tree of life?Eukaryotic tree of life?

• The divisions: The divisions:

– Ophistokonts (animals, fungi, microsporidia)Ophistokonts (animals, fungi, microsporidia)

– Amoebozoa (Dicty)Amoebozoa (Dicty)

– Chromalveolata Paramecium, Plasmodium but Chromalveolata Paramecium, Plasmodium but also diatomsalso diatoms

– ArchaeplastidaArchaeplastida

– ExcavataExcavata

– RhizariaRhizaria

• Historically: crown-group eukaryotes vs protistsHistorically: crown-group eukaryotes vs protists

• What is a complete genome; draft genomesWhat is a complete genome; draft genomes

• The divisions: The divisions:

– Ophistokonts (animals, fungi, microsporidia)Ophistokonts (animals, fungi, microsporidia)

– Amoebozoa (Dicty)Amoebozoa (Dicty)

– Chromalveolata Paramecium, Plasmodium but Chromalveolata Paramecium, Plasmodium but also diatomsalso diatoms

– ArchaeplastidaArchaeplastida

– ExcavataExcavata

– RhizariaRhizaria

• Historically: crown-group eukaryotes vs protistsHistorically: crown-group eukaryotes vs protists

• What is a complete genome; draft genomesWhat is a complete genome; draft genomes

AnimalsAnimalsAnimalsAnimals• Most primitive: spongesMost primitive: sponges

• Quite a number of genome sequences (of Quite a number of genome sequences (of dubious completeness)dubious completeness)

• Most primitive: spongesMost primitive: sponges

• Quite a number of genome sequences (of Quite a number of genome sequences (of dubious completeness)dubious completeness)

FungiFungiFungiFungi

• Many complete genomesMany complete genomes

• Broad, GenolevuresBroad, Genolevures

• Microsporidium (Microsporidium (E. cuniculiE. cuniculi))

• Mushrooms are Mushrooms are BasidomyctesBasidomyctes

• Together with animals: Together with animals: ophistokontsophistokonts

• Many complete genomesMany complete genomes

• Broad, GenolevuresBroad, Genolevures

• Microsporidium (Microsporidium (E. cuniculiE. cuniculi))

• Mushrooms are Mushrooms are BasidomyctesBasidomyctes

• Together with animals: Together with animals: ophistokontsophistokonts

AmoebozoaAmoebozoaAmoebozoaAmoebozoa

• Few genomesFew genomes

– Entamoeba histolyticaEntamoeba histolytica

– Dictyostelium discoideumDictyostelium discoideum

• Few genomesFew genomes

– Entamoeba histolyticaEntamoeba histolytica

– Dictyostelium discoideumDictyostelium discoideum

ArchaeplastidaArchaeplastidaArchaeplastidaArchaeplastida

• Second bacterial endosymbiosis event: Second bacterial endosymbiosis event: cyanobacteriacyanobacteria

• Green algae, red algae, plantsGreen algae, red algae, plants

• ~5 genomes ~5 genomes

• Second bacterial endosymbiosis event: Second bacterial endosymbiosis event: cyanobacteriacyanobacteria

• Green algae, red algae, plantsGreen algae, red algae, plants

• ~5 genomes ~5 genomes

ChromalveoatesChromalveoatesChromalveoatesChromalveoates

• Secondary endosymbios: plastidsSecondary endosymbios: plastids

• Very different speciesVery different species

• (diatoms (also commonly referred to as algae), (diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, oomycetes, paramecium, alvealotes, dinoflagelates)dinoflagelates)

• Quite some genomes (~10)Quite some genomes (~10)

• Secondary endosymbios: plastidsSecondary endosymbios: plastids

• Very different speciesVery different species

• (diatoms (also commonly referred to as algae), (diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, oomycetes, paramecium, alvealotes, dinoflagelates)dinoflagelates)

• Quite some genomes (~10)Quite some genomes (~10)

B

ExcavataExcavataExcavataExcavata

• Weird parasitesWeird parasites (Giardia, Trypanosome, (Giardia, Trypanosome, Leismania)Leismania)

• But also: But also: Naegleria gruberi: amoeboflagelateNaegleria gruberi: amoeboflagelate

• Weird parasitesWeird parasites (Giardia, Trypanosome, (Giardia, Trypanosome, Leismania)Leismania)

• But also: But also: Naegleria gruberi: amoeboflagelateNaegleria gruberi: amoeboflagelate

RhizariaRhizariaRhizariaRhizaria• Amoeboids + amoeboflagellates Amoeboids + amoeboflagellates

• produce shells which make up the vast majority produce shells which make up the vast majority of protozoan fossils. of protozoan fossils.

• No genomes (yet)No genomes (yet)

• Amoeboids + amoeboflagellates Amoeboids + amoeboflagellates

• produce shells which make up the vast majority produce shells which make up the vast majority of protozoan fossils. of protozoan fossils.

• No genomes (yet)No genomes (yet)

How are eukaryotes related ???How are eukaryotes related ???How are eukaryotes related ???How are eukaryotes related ???

• Historically: crown-group eykaryotes vs protists Historically: crown-group eykaryotes vs protists but now molecular evidencebut now molecular evidence

• Two hypothesis:Two hypothesis:

– In or just after excavataIn or just after excavata

– Inbetween ophistokonts/amoebozoa vs the Inbetween ophistokonts/amoebozoa vs the rest (unikont vs bikont), myosinsrest (unikont vs bikont), myosins

• Rhizaria?Rhizaria?

• phagotrophic origin of eukaryotes: an amoebe phagotrophic origin of eukaryotes: an amoebe with flagella? with flagella?

• Historically: crown-group eykaryotes vs protists Historically: crown-group eykaryotes vs protists but now molecular evidencebut now molecular evidence

• Two hypothesis:Two hypothesis:

– In or just after excavataIn or just after excavata

– Inbetween ophistokonts/amoebozoa vs the Inbetween ophistokonts/amoebozoa vs the rest (unikont vs bikont), myosinsrest (unikont vs bikont), myosins

• Rhizaria?Rhizaria?

• phagotrophic origin of eukaryotes: an amoebe phagotrophic origin of eukaryotes: an amoebe with flagella? with flagella?

b