The spread of the first introns in proto-eukaryotic paralogs

Abstract

Spliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20-35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.

Fig. 1. Characteristics of unique and shared LECA introns.

a The reconstruction of introns in LECA (Pfam orthogroups (OGs)), distinguishing unique LECA introns and shared LECA introns that likely originated before a duplication. Pfam OG1-3 represent three paralogous Pfam OGs that resulted from two duplications during eukaryogenesis, as indicated. b The comparisons of intron positions in KOGs within a cluster, identifying post-LECA introns, unique LECA introns and LECA introns shared between KOGs. KOG1-3 represent three paralogous KOGs in a cluster that resulted from two gene duplications during eukaryogenesis. c Fraction of shared LECA introns in the two datasets used in this study, in comparison with the fraction of shared introns as calculated in Sverdlov et al.. d Density plot showing the relative positions of introns in the alignment of a KOG. The three distributions are all significantly distinct from one another according to Kolmogorov–Smirnov tests. e Intron phase distributions in Pfam OGs and KOGs. All pairwise comparisons were significant, except shared LECA versus unique LECA Pfam introns (Supplementary Tables 1, 2). Numbers in c–e indicate the number of introns considered.

Fig. 2. Fraction of shared LECA introns between pairs of KOGs in a cluster with the same function.

Sixty-nine percent of pairwise comparisons were significant, including all but one with nuclear transport (Supplementary Data 3). Numbers indicate the number of LECA introns. Only functions with at least ten LECA introns and ten pairs are shown.

Fig. 3. Reconstruction of pre-duplication introns in Pfam duplications of different functions and cellular localisations.

a, b Fraction of duplications with introns traced to their pre-duplication state according to functional category (a) and cellular localisation (b). Thirty percent of pairwise comparisons of functions were significant (Supplementary Data 4). 14% of pairwise comparisons of localisations were significant, which were only comparisons including the endosome and cilium (Supplementary Data 5). Numbers indicate the number of duplications. Only functions and localisations with at least ten duplications are shown. c, d Excerpts from the gene trees of the adaptin (PF01602) (c) and SNF2 family (PF00176) (d) with the reconstructed presence of introns depicted. The triangles and names correspond to the Pfam OGs. The shared LECA introns in a Pfam OG are coloured and the gain and loss of these introns is mapped onto the phylogeny. The number of unique LECA introns is indicated in grey. Ultrafast bootstrap support values lower than 100 are shown. The branch with a prokaryotic sequence that fell between the Pfam OGs in (c) is shown as a dotted line. The shared intron in AP4 ε that is marked with an asterisk was classified as a U12-type intron. Although the phylogenetic position of the two COPI subunits is probably incorrect, the inferred intron gains and losses in these trees are largely unaffected by topology changes.

Fig. 4. Reconstruction of pre-duplication introns in Pfam duplications of different phylogenetic origins.

a Fraction of duplications with introns traced to their pre-duplication state for different phylogenetic origins. Sixty percent of pairwise comparisons were significant, including all but one comparison with alphaproteobacterial duplications (Supplementary Table 6). b Fraction of the most ancestral duplication in an acquisition or invention with introns traced to their pre-duplication state. Differences between groups were not significant. Numbers indicate the number of duplications.