Introduction
Repetitive sequence (RS) elements are characterized as multi-copied sequences in two broadly defined classes: satellite sequences (SSs), including both micro-satellites and mini-satellites, and transposable elements (TEs) that are characterized based on sequence identity and structure, biogenesis, insertion site preference, and degree of redundancies.1,2 The RSs are evolutionarily active and show significant influences on the structures of genes and genomes, and are thus highly relevant to biological functions.3,4 It has been reported that TE-free regions are negatively selected for certain regulatory elements throughout vertebrate genomes, although the conservation of the sequence contents is often variable.5,6 Furthermore, TEs have different distributions among exonic, intronic, and intergenic regions.7 Indeed, a small number of TE classes are still active, generating population differentiation,8 and the compositional dynamics of genomic sequences exhibits step-by-step evolutionary changes as a consequence of competitions between host genomes and parasitic sequences.3 In addition, TE transposition often serves as a driving force for the conversion of introns into exons or gaining novel introns as well as alternatively spliced transcripts.9–11 Therefore, new sequence integration and the balance of exons and introns in number, length, and ordinal position of a gene provide basic materials for species evolution.12
Different subfamilies of TEs have seemingly diverse influences on genes and genomes by changing sequence length to variable extents. Specifically, due to the distinction between “copy-and-paste” of retrotransposons and “cut-and-paste” mostly used by DNA transposons, the former should be a primary player in the event of genome size increase.2 Introns are considered as the major “warehouse” of TEs11,13 and certain families of TEs are observed to correlate with functional genes, such as between mammalian interspersed repeats (MIRs) and immune genes.13 Exploiting the relationship between sequence composition and polymorphism, we noticed that minimal introns (introns in a minimal size range) have unique features distinct from larger introns and demonstrated how these smaller introns escape from TE-driven insertions and also largely free from SS-driven intron expansion.14–16 As many vertebrate genomes have now been sequenced, we are able to address more questions on TE- and SS-driven intron expansions in different vertebrate lineages. In particular, we would like to understand how intron expansion relates to gene functions among the three subgroups of mammals—primates, large mammals, and rodents—and what are the roles of mutation and natural selection played in the course of genome evolution.