Eugene Koonin 2004 Bioinformatics talk.ppt

Evolution of eukaryotic genomes: remarkable conservation and massive loss of genes and introns Evolution of introns and the exonic structure of eukaryotic genes Tempo and mode of intron evolution remain poorly understood. When did introns invade eukaryotic genes: prior to the origin of eukaryotes (introns early), early in eukaryotic evolution, or late? The common ancestor of animals, plants and fungi: intron-rich or intron-poor? What fraction of introns is conserved over long evolutionary spans? Origin of introns The intron-early hypothesis suggests that introns existed before the divergence of prokaryotes and eukaryotes (W. Gilbert). The intron-late hypothesis posits that introns were inserted into eukaryotic genes after this divergence (T.Cavalier-Smith, Doolittles, J.Palmer) a Pf Sc Sp At Ce Dm Ag Hs Pf 450/971 2 48 137 50 46 54 145 Sc 1 22/46 7 3 3 3 4 6 Sp 34 6 450/839 209 98 114 111 308 At 97 2 147 2933/5589 353 255 254 1148 Ce 33 2 63 240 1468/3465 315 312 948 Dm 32 1 72 161 179 723/1826 787 802 Ag 36 1 62 158 176 382 675/1768 771 Hs 104 3 207 787 557 433 403 3345/6930 Conservation of intron positions among eukaryotes Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV.Curr Biol. 2003 Sep 2;13(17):1512-7. Example: KOG0473 – ribosomal protein L37 Alignment with mapped intron positions is converted to a matrix of intron presence/absence Conserved intron positions - phylogenetic signal Example: KOG0419 - TCP-1a subunit of chaperonin complex The only intron among 684 genes conserved in 7 species Matrices for all analyzed genes were concatenated and employed to build a single tree - 684 KOGs, 7236 intron positions Phylogenetic tree of crown group eukaryotes based on conservation of intron positions: parsimony The topology of this tree is a bit unexpected... The phylogenetic parsimony tr