The insertion profiles of TEs and SSs are diverse among the vertebrate genomes
We evaluated the expansion strength of TEs and SSs in introns based on the ratio of the repeat length over the corresponding RS-free length (Table 6). We found that zebrafish has the strongest expansion strength among TS, T, and S genes, whereas chicken has the weakest strength in TS and S genes and anole has the weakest strength in T genes. In the mammals, opossum has the strongest strength in TS and S genes but T genes have the most strength in platypus. A striking observation is the fact that the strength of TS genes is greater than the sum of both T and S genes in the mammals, and we saw the opposite phenomenon in the non-mammalian vertebrates (Table 6).
When integrating the content of intronic repeats in individual genes based on orthology (unique homologous gene in each species), we discovered different topological structures (Fig. 8). The shared clusters between the two trees are the human-orangutan and the mouse-rat clades, the distant relationship to chicken, and the approximation of zebrafish to placental mammals as compared to the other three non-mammalian vertebrates. With regard to TEs, the primates and the large mammals are remarkably distinct from the rest species and are closer to the mouse-rat clade as compared to guinea pig. With regard to SSs, opossum is clustered with the primates as well as the rodents and the four large mammals rather than the other primitive mammal, platypus.