Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

A case where gene age may have been overestimated is that of taxon 3 (betacoronavirus I gene). Our analysis suggested that the I and ORF9b genes have a common origin (see supplementary information, Supplementary Material online, case 3) despite their different lengths (98aa and 207aa, respectively) and lack of significant sequence similarity (not shown). This inference is based on assuming functionality for the unannotated ORFs in five closely related genomes (supplementary fig. S4, Supplementary Material online) . Consequently, we calculated the age of the I gene by considering the node common to I and ORF9b (marked with blue line, supplementary fig. S5 , Supplementary Material online, group 3). In the alternative scenario where these two genes have independent origins, their estimated age would be reduced. Nevertheless, the overall pattern of the results would remain unchanged (not shown). Another caveat to our study is that RNA secondary structure, and selection pressure for high protein expression level may be partly responsible for the differences we observed in codon usage (Plotkin and Kudla 2011) .