Fig. 2

In-frame UAG codons in protein-coding genes of the rhizarian exLh and I. spirale. a An example of a rhizarian exLh gene with several in-frame UAG codons: multiple sequence alignment of orthologs of the Bat1 protein (spliceosome RNA helicase). b Relative frequency of hyperconserved positions (at least 90% amino acid identity across orthologs from 250 representatives of main eukaryotic groups in the alignment) corresponding to UAG-containing sites in the rhizarian exLh transcripts. c An example of a I. spirale gene with several in-frame UAG codons: multiple sequence alignment of orthologs of the Polr2a protein (also known as RNA polymerase II subunit RPB1). d Relative frequency of hyperconserved positions (at least 90% amino acid identity across orthologs from 54 representatives of main eukaryotic groups in the alignment) corresponding to UAG-containing sites in the rhizarian exLh transcripts. e, f Dominant amino acid identity at conserved alignment positions (defined using 90% and 50% threshold) in a broad-scale comparison of I. spirale sequences with eukaryotic homologs. e Positions corresponding to in-frame UAG codons in I. spirale sequences. f Positions corresponding to canonical glutamine codons (CAG, CAA) in I. spirale sequences. In Fig. 2a and c , only selected segments of the full alignments (separated by double slashes) are shown for simplicity. Asterisks indicate positions with in-frame UAG codons in the underlying coding sequences. In Fig. 2b and d , the hyperconserved positions are sorted according to the respective hyperconserved amino acid residue (only four most frequent position classes are shown). Source tables for Fig. 2b and d including data from read mapping are available in Additional file 1: Table S1D and S2C