Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

Several previous studies have examined the codon usage of individual or small groups of overlapping genes (McGeoch et al. 1985; Keese and Gibbs 1992; Pavesi et al. 1997; McVeigh et al. 2000; Lee et al. 2010) , their rates of evolution (Mizokami et al. 1997; Sanz et al. 1999; Jordan et al. 2000; Fujii et al. 2001; Nekrutenko et al. 2005 Zaaijer et al. 2007 ). Overall, our observations agree with those of previous studies-ancestral and de novo genes differ in these properties. Nevertheless, we were able to improve on these studies in several ways. First, by examining the phylogenetic distribution of overlapping gene pairs, we were able to identify reliably (see later) which of the two genes is ancestral and which one is the de novo gene. Second, our new method allowed us to estimate the relative age of origin of de novo genes and to correlate this age with several quantifiers of their evolutionary dynamics. Thus, it allowed us to analyze how the evolutionary forces affecting de novo genes change over time. Third, we used a larger data set than most studies mentioned earlier, which were carried out on individual genes. Fourth, we used a method specifically tailored to overlapping genes (Sabath et al. 2008) to study the selective constraints these genes are subjected to. Other methods can give misleading results when applied to overlapping genes (Holmes et al. 2006; Suzuki 2006; Pavesi 2007; Sabath et al. 2008 ).