Transposable elements as drivers of genomic and biological diversity in vertebrates

Abstract

Comparative genomics has revealed that major vertebrate lineages contain quantitatively and qualitatively different populations of retrotransposable elements and DNA transposons, with important differences also frequently observed between species of the same lineage. This is essentially due to (i) the differential evolution of ancestral families of transposable elements, with evolutionary scenarios ranging from complete extinction to massive invasion; (ii) the lineage-specific introduction of transposable elements by infection and horizontal transfer, as exemplified by endogenous retroviruses; and (iii) the lineage-specific emergence of new transposable elements, as particularly observed for non-coding retroelements called short interspersed elements (SINEs). During vertebrate evolution, transposable elements have repeatedly contributed regulatory and coding sequences to the host, leading to the emergence of new lineage-specific gene regulations and functions. In all vertebrate lineages, there is evidence of transposable element-mediated genomic rearrangements such as insertions, deletions, inversions and duplications potentially associated with or subsequent to speciation events. Taken together, these observations indicate that transposable elements are major drivers of genomic and biological diversity in vertebrates, with possible important roles in speciation and major evolutionary transitions.

Transposable elements as a potential source for understanding the fish genome

“…9 All types of transposable elements can be found within the fish genome, where a diversity level not found in mammals and birds is observed. 10 Regarding chromosome organization, TEs can be organized in clusters or dispersed throughout the genome.…”

Transposable elements and an epigenetic basis for punctuated equilibria

“…(57) These same sequences endow TEs with an unparalleled capacity to promote genetic innovation in the host. TEs not only function as mediators of gene duplication and recombination, but also provide a rich reservoir of sequences that can be recruited to function for the host genome, (58) a process known as ''molecular domestication.'' Screening of genomic sequences with repetitive element detection software has dramatically increased the number of host coding sequences known to have evolved from TEs.…”

“…Screening of genomic sequences with repetitive element detection software has dramatically increased the number of host coding sequences known to have evolved from TEs. (57)(58)(59) Domestication of TE coding sequences has been especially important in the evolution of the mammalian placenta, with genes independently recruited from two distinct types of retro-element sequences, retrotransposon gag genes and endogenous retroviral envelope (env) sequences. (60) Therian mammals (marsupials and eutherians) diverged from the egg-laying monotremes $170 million years (My) ago (Mya).…”

Genomic Organization Under Different Environmental Conditions:Hoplosternum Littoraleas a Model

“…7,8 Repetitive DNA sequences play key roles in adaptive processes in many organisms because they are less vulnerable to selective pressures compared to single-copy sequences. 4,5,[8][9][10][11][12] Such adaptive processes may be related to genetic variability, which enables a population to adapt to an environment. 13,14 However, the environment has experienced severe damage resulting from anthropic activity, 15 and aquatic biota is constantly exposed to numerous toxic substances released daily into the water.…”