Fig 1.
Coulson plot showing the presence/absence of exon junction complex components eIF4AIII, Magoh, Y14 and MLN51 in selected species representative of the eukaryotic diversity.
The coloured segments of the plot indicates that the protein is present and the numeral denotes the number of homologues identified. The blank segments denote that homologues of these proteins were not identified in the corresponding species.
Fig 2.
Intron density/EJC (eIF4AIII, Magoh, Y14 and MLN51) distribution among eukaryotes.
The intron density (here: average number of introns per gene) is plotted for different eukaryotes. Adapted from Roy and Gilbert (2006). From top right: Trypanosoma brucei, Leishmania major, Giardia lamblia, Trichomonas vaginalis, Cyanidioschyzon merolae, Cryptosporidium parvum, Saccharomyces cerevisiae, Candida albicans, Paramecium aurelia, Schizosaccharomyces pombe, Plasmodium falciparum, Plasmodium yoelii, Entamoeba histolytica, Dictyostelium discoideum, Thalassiosira pseudonana, Drosophila melanogaster, Caenorhabditis briggsae, Caenorhabditis elegans, Chlamydomonas reinhardtii, Oryza sativa, Arabidopsis thaliana, Mus musculus, Homo sapiens. The EJC proteins are colour coded to show presence/absence in the various species represented: eIF4AIII is conserved and present in all species Magoh and Y14 are present mostly in intron-rich species, very diverged (represented in paler colours) as seen in Trypanosoma brucei and Leishmania major or not present in intron-poor species MLN51 is present only in animals.
Fig 3.
Coulson plot showing the presence/absence of eIF4A, eIF4E, eIF4G & PABP in selected species representative of the eukaryotic diversity.
The coloured segments of the plot indicates that the protein is present and the numeral denotes the number of homologues identified. The blank segments denote that homologues of these proteins were not identified in the corresponding species.
Fig 4.
Phylogenetic analysis of eIF4E proteins in selected excavates using Mr Bayes (Posterior probability), PhyML & RaxML (Maximum Likelihood methods).
The tree is shown in the Bayesian topology. Numerical values at the nodes of the tree (x/y/z) indicate statistical support by MrBayes, PhyML and RAxML, posterior probability, bootstrap and bootstrap, respectively. Values for highly supported nodes have been replaced by symbols as indicated. There are no values on branches that are not well supported.
Fig 5.
Phylogenetic analysis of eIF4G in selected eukaryotes using Mr. Bayes (Posterior probability).
Values for highly supported nodes have been replaced by symbols as indicated. Numbers indicate posterior probability values for Mr Bayes.
Fig 6.
Phylogenetic analysis of PABP in selected eukaryotes using Mr Bayes (Posterior probability), PhyML & RaxML (Maximum Likelihood methods).
Values for highly supported nodes have been replaced by symbols as indicated. Numbers indicate Bayesian posterior probabilities and bootstrap support for PhyML and RAxML respectively.
Fig 7.
Phylogenetic analysis of mRNA degradation proteins in selected excavates.
A) Phylogenetic analysis of NOT1, NOT5, NOT9 and NOT10 proteins using Homo sapiens NOT1 as an outgroup. Numbers indicate Bayesian posterior probabilities and bootstrap support for PhyML and RaxML respectively. B) Phylogenetic analysis of XRN proteins using Mr Bayes (Posterior probability). Values for highly supported nodes have been replaced by symbols as indicated.
Fig 8.
A schematic diagram of the origins, secondary loss, and expansions of key subunits discussed in this study, plotted onto a schematic tree of the eukaryotes [15, 22, 10].
The most probable position of each event was identified using Mesquite [80]. A full tree, containing all of the species used for analysis in this study, is shown in figure S6 Fig. The following proteins analysed in this study were found to be present in the LECA using parsimony analysis on Mesquite from both root positions [22, 10]: EJC proteins (eIF4AIII, Magoh, Y14); Translation Initiation factors (eIF4AI, eIF4E, eIF4G); PABP & mRNA degradation proteins analysed in this study. The exception is the EJC protein, MLN51 which was found to be present in Opisthokonta to the exclusion of Fungi.