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

Fish represent over half of vertebrate species and harbor diverse repetitive elements. Although many fish genomes have been sequenced, the repetitive elements and their roles remain largely unknown. In this study, we conducted extensive analyses of repetitive elements in the channel catfish (Ictaluru punctatus) and performed comparative analyses of repetitive elements with 51 other fish. In channel catfish, the repetitive elements account for 42.88% of the total genome and are composed of 72 subclasses with DNA/TcMAr-Tc1 and microsatellites being the two dominant types. Comparative analyses revealed that genomes of diadromous fish such as eels, salmon and some freshwater species such as catfish, cavefish are also abundant in DNA/TcMAr-Tc1 and microsatellites. Interestingly, Class II transposons tend to be more in freshwater teleost than those seawater living teleost (W=393, p-value=2.1e-05), suggesting the freshwater environments are more favorable for the Class II transposon proliferation. In contrast, the tandem repeats were observed to be more prevalent in the genomes of teleost living in sea than those freshwater teleost species (W=395, p-value=1.6e-05), indicating that salty environment can be more favorable for DNA polymerase slippage. Notably, the Class I transposons were observed to be the most abundant types in primitive species such as Cartilaginous and Cyclostomata, in dramatic contrast with their low presence in teleost (W=235, p-value=1.4e-04). In addition, the proportion of repetitive elements was found to be positively correlated with the genome size (r=0.6, p-value=1.28e-06). Our results extend understanding of repetitive elements, their composition, distribution and potential association with evolutionary adaptations to various environments.