Teleost Fish Genomes Contain a Diverse Array of L1 RetrotransposonLineages That Exhibit a Low Copy Number and High Rate of Turnover

Abstract

Retrotransposable elements exhibit a wide range of variation in population dynamics, abundance, and lineage diversity among host genomes across taxa. This range of diversity is illustrated by a single well-defined constituent monophyletic clade of L1 non-LTR retrotransposons that is shared between mammalian and teleost fish genomes. Despite the clear phylogenetic relationships that exist between mammalian and teleost L1 sequences, these elements exhibit markedly different dynamics within their respective taxa. While mammalian genomes typically contain a single, abundant lineage of L1 elements that traces millions of years of evolution, the zebraflsh genome was recently shown to exhibit a high diversity of ancient lineages coexisting at a very low copy number and apparently exhibiting a high rate of turnover. In the present study, a combination of degenerate PCR, lineage-specific PCR, and genomic Southern blot analysis is utilized to demonstrate high L1 lineage diversity, low copy number, and a high proportion of polymorphic inserts in the genomes of the killifish species, Fundulus heteroclitus. Additional species surveyed by degenerate PCR include Cyprinodon variegatus, Rivulus marmoratus, and Menidia beryllina. These results further support the generality of the differences that exist in host-element dynamics between teleost fish and mammalian genomes with regard to L1 retrotransposons.

Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

“…Five clades show signs of very recent activity, and two of these clades, L1 and L2, contain numerous simultaneously active families. This situation is similar to that in fish [Volff et al, 2003;Duvernell et al, 2004]. The scarcity of divergent elements and the abundance of very young inserts indicate that the vast majority of retroposons do not reach fixation in the Anolis genome, suggesting a rapid turnover of elements [Novick et al, 2009].…”

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

“…Although TE family numbers are lower in mammals than in fish species, TE copy numbers are generally much higher in mammals than in fishes (Volff 2005). Therefore, TEs in fish genomes appear to have undergone a higher turnover than in the mammalian genomes (Duvernell et al 2004), which is similar to that observed in Drosophila (Eickbush and Furano 2002) . …”

The transposable element profile of the Anolis genome

“…26 For instance, in Anolis the L1 clade is represented by 20 active families, the origins of which predate the split between reptiles and mammals. Each L1 family is represented by a small number (<100) of very similar copies, reminiscent of the diversity reported in the zebrafish genome 21,28 but drastically more diverse than in modern mammals. 29 A recent study of the newly discovered Ingi clade of non-LTR retrotransposons found these elements in the Anolis genome, suggesting there may be more of these kinds of TEs to be discovered in this genome.…”

“…At the other end of the spectrum, some teleostean fish genomes are considerably smaller than mammalian genomes yet contain a comparatively more diverse TE profile, comprised of families usually represented by small numbers (<100) of very similar copies. [20][21][22] is the fact that the majority of these families have recently been active or is still active. Thus the anole genome is exposed to a tremendous level of TE activity, unparalleled among extant amniotes and possibly among vertebrates.…”