Teleost Fish Genomes Contain a Diverse Array of L1 Retrotransposon Lineages 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.

Department(s)

Biological Sciences

Keywords and Phrases

controlled study; Cyprinodontiformes; genome; mammal; nonhuman; nucleotide sequence; polymerase chain reaction; retroposon; Southern blotting; teleost; Animals; Base Sequence; Blotting; Southern; Cluster Analysis; Databases; Genetic; DNA Primers; Evolution; Molecular; Long Interspersed Nucleotide Elements; Molecular Sequence Data; Phylogeny; Sequence Analysis; DNA; Smegmamorpha; Variation (Genetics); Cyprinodon; Cyprinodon variegatus; Danio rerio; Fundulus; Fundulus heteroclitus; Mammalia; Menidia; Menidia beryllina; Rivulus; Rivulus marmoratus; teleost fish; Teleostei; transposons; Fish; L1; LINE; Retrotransposon

International Standard Serial Number (ISSN)

0022-2844

Document Type

Article - Journal

Document Version

Citation

File Type

text

Language(s)

English

Rights

© 2004 Springer New York, All rights reserved.

Publication Date

01 Sep 2004

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