Comparative Genome Analysis of 52 Fish Species Suggests Differential Associations of Repetitive Elements with Their Living Aquatic Environments

Repetitive elements are important for genome evolution. Here we report differential association of repetitive elements with the genomes of fish living in different aquatic environments. Specifically, Class II transposons are more abundant in freshwater bony fish than in marine bony fish. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, Class I transposons were more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. Our results suggested long and active transposition of Type II transposons in freshwater fish during evolution and greater levels of polymerase slippage/low levels of fidelity during DNA replication in marine fish. These findings indicate potential roles of repetitive elements not only in shaping up the genome architecture, but also in adaptation of aquatic species to their environments.