Conserved Introns

Conservative Genome Evolution

Evolutionary Conservation of Introns

An important component of eukaryotic genomes. 25% of the human genome 95% of the human transcriptome [Venter et

al., (2001)]

Numerous cis-regulatory elements reside within introns. Alternate transcripts greatly magnify

transcriptome complexity. Introns foster genetic recombination.

FUNGIPLANTAE METAZOA

PlasmodiumArabidopsis Caenorhabditis

Saccharomyces

AnophelesDrosophila

Homo Surprisingly, Arabidopsis appeared

most similar to human. We added Nematostella to these taxa

and performed a comparable analysis on a subset of the same orthologous genes (n=348 genes).

Rogozin et al. (2003) compared the location of introns in 684 orthologous genes across a number of model eukaryotes. APICOMPLEXA

Evolutionary Conservation of Introns

Percentage of Shared Introns

Pf At Sp Nv Ce Dm Ag HsPfAtSpNvCeDmAgHs

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159At 1076Sp 173Nv 1459Ce 560Dm 260Ag 269Hs 1246

Percentage of Shared IntronsQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159At 1076Sp 173Nv 1459Ce 560Dm 260Ag 269Hs 1246

Percentage of Shared IntronsQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159At 1076Sp 173Nv 1459Ce 560Dm 260Ag 269Hs 1246

Percentage of Shared IntronsQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159At 1076Sp 173Nv 1459Ce 560Dm 260Ag 269Hs 1246

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

Percentage of Shared IntronsQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159 3% 3% 3% 2% 2% 3% 2%At 1076 5% 17% 7% 5% 5% 16%Sp 173 6% 4% 7% 6% 7%Nv 1459 14% 9% 10% 47%Ce 560 11% 11% 15%Dm 260 43% 13%Ag 269 12%Hs 1246

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

Percentage of Shared IntronsQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159 3% 3% 3% 2% 2% 3% 2%At 1076 5% 17% 7% 5% 5% 16%Sp 173 6% 4% 7% 6% 7%Nv 1459 14% 9% 10% 47%Ce 560 11% 11% 15%Dm 260 43% 13%Ag 269 12%Hs 1246

Percentage of Shared Introns

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159 3% 3% 3% 2% 2% 3% 2%At 1076 5% 17% 7% 5% 5% 16%Sp 173 6% 4% 7% 6% 7%Nv 1459 14% 9% 10% 47%Ce 560 11% 11% 15%Dm 260 43% 13%Ag 269 12%Hs 1246

Percentage of Shared Introns

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159 3% 3% 3% 2% 2% 3% 2%At 1076 5% 17% 7% 5% 5% 16%Sp 173 6% 4% 7% 6% 7%Nv 1459 14% 9% 10% 47%Ce 560 11% 11% 15%Dm 260 43% 13%Ag 269 12%Hs 1246

Percentage of Shared Introns

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Pf At Sp Nv Ce Dm Ag HsPf 159 3% 3% 3% 2% 2% 3% 2%At 1076 5% 17% 7% 5% 5% 16%Sp 173 6% 4% 7% 6% 7%Nv 1459 14% 9% 10% 47%Ce 560 11% 11% 15%Dm 260 43% 13%Ag 269 12%Hs 1246

Percentage of Shared Introns

(Introns shared by A & B)= (Introns shared by A &

B)(Introns unique to

A)(Introns unique to

B)+ +

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Clustering of taxa based on shared introns Parsimony analysis of intron presence/absence.

1 = intron present at a given location (±2 nt).

0 = intron absent. Human and sea

anemone are grouped to the exclusion of all other animals in the analysis.

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

Mapping intron gain & loss on the organismal phylogeny

ACCTRAN character state optimization.

Suggests that the cnidarian-bilaterian ancestor was intron-rich. (880 introns)

And that there have been numerous intron losses in the line(s) leading to the model protostomes.

Finer taxonomic sampling is needed.

abundant introns

many intron losses

relative stability

Sullivan, Reitzel and Finnerty, Genome Informatics (2006)