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