Eukaryotic Intron LossTobias Mourier & Daniel C. Jeffares

Introns

Pre-mRNA

DNA

mRNA

Intron evolution

Bacteria -introns

Archaea -introns

Eukaryota +introns

Introns early/Introns late

Intron evolution

Intron evolution

ATGAAGCGATGT

Met Lys Arg Cys

Intronfase 0

Intronfase 1

Intronfase 2

“Exon Theory of Genes”

Eukaryotic intron loss

Fink GR, Cell 49, 5 (1987):

Introns i Saccharomyces cerevisiae ligger oftest i 5’ (starten) af genet

Introns er tabt gennem rekombination med revers transkriberet cDNA

Eukaryotic intron loss

mRNA

cDNA

Revers transkription

Eukaryotic intron loss

mRNA

cDNA

Eukaryotic intron loss

mRNA

cDNA

Probability of cDNA coverage

5’ Position 3’

Eukaryotic intron loss

mRNA

cDNA

Probability of cDNA coverage

5’ Position 3’

Eukaryotic intron lossMammals

Homo sapiensRattus norvegicusMus musculusVertebrates

Takifugu rubripesDanio rerioInvertebrates

Caenorhabditis elegansAnopheles gambiaeDrosophila melanogasterPlants

Arabidopsis thalianaOryza sativa japonica

Fungi

Neurospora crassaSchizosaccharomyces pombeSaccharomyces cerevisiaeEncephalitozoon cuniculi(Magnaporthe grisae)Alveolates

Plasmodium falciparumPlasmodium yoelii yoeliiSlime mold

Dictyostelium discoideum (chr. II)Red algae

Guillardia theta nucleomorph

~250.000 gener ~900.000 introns

Eukaryotic intron loss

A

B

Relative Intron Position = A/B

12

34

56

78

910

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Homo sapiens (8.4) Rattus norvegicus (8.3)

Mus musculus (7.6) C. elegans (5.2) A. thaliana (4.2)Oryza sativa (3.2)

Takifugu rubripes (3.1) Danio rerio (3.0) Anopheles gambiae (2.8) D. melanogaster (2.7) Magnaporthe grisea (1.9) Neurospora crassa (1.7)Plasmodium falciparum (1.3)

Dictyostelium discoideum II (1.2) Plasmodium yoelii yoelii (1.1)Schizosaccharomyces pombe (0.95)

Saccharomyces cerevisiae (0.045)Guillardia theta nucleomorph (0.035)

Encephalitozoon cuniculi (0.0075)

Relative intron position

5’ 3’

Fract

ion o

f in

tron

s

12

34

56

78

910

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Relative intron position

5’ 3’

Fract

ion o

f in

tron

s

Intron erhvervelseeller

Intron tab

0

0.1

0.2

0.3

0.4

0.5

0.6

0 1 2 3 4 5 6 7 8 9

Intron/gene ratio

Average relative intron position

5’ Intron erhvervelse

3’ Intron tab

Insertions bias?Positions-afhængig selektion?

Intron erhvervelse Intron tab

Intron erhvervelse Intron tab

Intron erhvervelse Intron tab

Eukaryotic intron lossMammalsHomo sapiensRattus norvegicusMus musculusVertebratesTakifugu rubripesDanio rerioInvertebratesCaenorhabditis elegansAnopheles gambiaeDrosophila melanogasterPlantsArabidopsis thalianaOryza sativa japonica

FungiNeurospora crassaSchizosaccharomyces pombeSaccharomyces cerevisiaeEncephalitozoon cuniculi(Magnaporthe grisae)AlveolatesPlasmodium falciparumPlasmodium yoelii yoeliiSlime moldDictyostelium discoideum (chr. II)Red algaeGuillardia theta nucleomorph

Sidste fælles stamform?

Johnson PJ, Proc Natl Acad Sci USA 99, 3358 (2002)

Dacks JB, Doolittle WF, Cell 107, 419 (2001)

SSU rRNA

Stechmann A, Cavalier-Smith T, Science 297, 89 (2002)

Gene fusion

Baldauf SL, Science 300, 1703 (2003) Konsensus (molekylære & strukturelle data)

Få introns i encellede eukaryoter er en afledt karakter

Den sidste fælles stamform (sidste fælles eukaryot?) var intron-rig

Eukaryotic intron loss