Figure 1.
Examples of a species with (A) strong consensus structures (S. cerevisiae), and (B) weakly conserved structures (human).
Figure 2.
Phylogenetic relationship between the species included in this study.
Consensus phylogenetic tree of the species included in this study. Red species names and discontinuous branches indicate intron-poor species. Note that representatives of all eukaryotic supergroups have been included in this study. Based on [47],[48].
Table 1.
Putative branch point consensus in the 16 studied intron-poor species.
Table 2.
Intron features for the 50 eukaryotic species included in this study.
Figure 3.
Relation between branch point site consensus strength and intron number.
(A) Percentage of introns with the most common BP-like hexamer across eukaryotes. Dark colored bars show the percentage of introns with the most common branch-point hexamer; light colored bars show the additional introns allowing for two-fold degeneracy at one of the six sites. The left red bar separates species with ‘strong’ BP motifs (>50% of introns) from species with weaker BP motifs. The right red bar separate extremely intron-poor species (< 0.15 introns per gene). Asterisks (*) mark the two exception to the correspondence between the two variables (strong BP/intron-poor vs. weak BP/intron-rich). (B) Logarithm of total intron number (Y-axis) and percentage of introns showing the most common potential branch point motif with one site two-fold degeneracy (X-axis) are plotted for all fully sequenced studied genomes. The species cluster in two different groups (with two exceptions) - intron-rich/weak BP consensus, intron-poor/strong BP consensus. The two intron-poor species not showing strong consensus branch points, G. thetha NM and C. parvum, are labeled. The line corresponds to a lineal regression analysis, showing the negative correlation (r = −0.75) between intron numbers and branch point consensus conservation.
Table 3.
Intron signal features for different intron subsets of O. lucimarinus.
Figure 4.
Highly constraint BP-AG distances in Y. lipolytica and T. vaginalis.
(A) 3′ intron boundary in Yaworria lipolytica. (B) 3′ intron boundary in Trichomonas vaginalis. Note that the difference between both consensus is the existance of 1 (Y. lipolytica) or 2 (T. vaginalis) AC dinucleotides between the BP motif and the terminal AG. Consensus sequence for G. lamblia is similar to T. vaginalis. (C) 3′ intron boundary for confirmed introns from non-chromosome 2 genes in O. lucimarinus. (D) 3′ intron boundary in C. elegans.
Figure 5.
Phylogenetic distribution of BP-AG distance across hemiascomicetous yeasts.
For each species, the distribution represents the fraction of introns with a certain distance to the AG from base -50 (most left) to base -1 (most right, terminal G). Grey background highlights relative lack of constraint BP-AG distance, and broken lines show the lineages that likely experienced the evolution of BP-AG distance constraint.
Table 4.
Intron signal features.
Figure 6.
Characteristic patterns of polyT motif distributions across eukaryotes.
Examples of: (A) Most common and widely distributed pattern. PolyT motifs concentrate at the 3′ of the introns. Observed in plants, animals, apicomplexa and heterokonts. (B) Pattern characteristic of most fungi and in T. pseudonana, characterized by relatively uniform polyT distribution. (C) Pattern of some intron-poor species. (D) Pattern observed in amebozoa and in the fungus U. maydis. Species included in the study: Homo sapiens (Hsap); Caenorhabditis elegans (Cele); Drosophila melanogaster (Dmel); Strongylocentrotus purpuratus (Spur); Arabidopsis thaliana (Atha); Oryza sativa (Osat); Plasmodium falciparum (Pfal); Phytophthora ramorum (Pram); Schizosaccharomyces pombe (Spo); Aspergillus fumigatus (Afu); Giberella zeae (Gzeae); Cryptococcus neoformans (Cne); Candida glabrata (Cgla); Eremothecium gossypii (Egos); Debaryomyces hansenii (Dhans); Yarrowia lipolytica (Ylip); Cryptosporidium parvum (Cpar); Saccharomyces cerevisiae (Sce); Kluyveromyces lactis (Klact); Dictyostelium discoideum (Ddis); Entamoeba hystolitica (Ehys); Ustilago maydis (Umay).