Gene content of the lsr operon was manually checked in each strain to confirm the presence of functional genes, identify misannotations, and characterize pseudogenes (identification of truncation, stop codon, and inserted sequences).
The splice mutation described in this study results in severely reduced expression of wild-type GBP5 and a frameshift that leads to an early stop codon and truncation of the 88 C-terminal amino acids.
Nonsense mutations leading to a premature stop codon and truncation of the predicted protein product were found in 25 strains and missense mutations leading to an amino acid change were found in 27 strains.
However, a mutation was identified in Pxdn cDNA (cDNA: T3816A in exon 19; Cys1272X; Fig. 1C), which causes a premature stop codon; the truncation is predicted to affect the C-terminal region of the peroxidase domain of Peroxidasin and the downstream von-Willebrand domain.
* Some genes contain frame shifts, stop codons or truncations (details in additional file 2).
Among the genes that underwent pseudogenization there are ycf68, ycf1 and rps19, which showed incomplete duplication in the IRA/IRB and LSC junction regions with loss of function due to accumulation of premature stop codons or truncations.
Interestingly, in sea urchin, the ancestral exon 11 splice site has been lost, implying constitutive use of the new STOP codon and protein truncation.
Among genes with non-synonymous changes, MAP2K3 contained a homozygous variant that introduced a premature stop codon resulting in truncation of most of the MAP2K3 kinase domain.
Computational analysis of TRAIL- α and its novel alternative splice variants showed that loss of exon 3 resulted in a frame shift generating a stop codon with consecutive truncation in the extracellular domains of both TRAIL- β and - γ.
In all species, the ENVV2 gene is intact, whereas the ENVV1 gene is preserved only in chimpanzee and rhesus macaque, where it exhibits a full-length ORF with no C-terminal truncation or stop codons.
