Abstract
BackgroundSeveral studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster), whereas putatively active sequences are present in others (D. simulans). Combining experimental and population analyses with the sequence analysis of the 12 Drosophila genomes, we have investigated the evolution of Helena, and propose a possible scenario for the evolution of this element.ResultsWe show that six species of Drosophila have the Helena transposable element at different stages of its evolution. The copy number is highly variable among these species, but most of them are truncated at the 5' ends and also harbor several internal deletions and insertions suggesting that they are inactive in all species, except in D. mojavensis in which quantitative RT-PCR experiments have identified a putative active copy.ConclusionOur data suggest that Helena was present in the common ancestor of the Drosophila genus, which has been vertically transmitted to the derived lineages, but that it has been lost in some of them. The wide variation in copy number and sequence degeneration in the different species suggest that the evolutionary dynamics of Helena depends on the genomic environment of the host species.
Highlights
Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated
Considerable internal deletions have previously been reported in the inactive copies of several non-long terminal repeat (LTR) retrotransposons [10], and this deletion mechanism seems to act at an high rate, since sequences that are similar at the nucleotide level may have very different internal deletions [10,11,18,19]
Identification and analysis of reference copies Using the full-length copy of Helena already identified in the draft sequence of the D. simulans genome [18], and 23 reverse transcriptase (RTase) fragments of the melanogaster species group [10], we performed a search for Helena-like elements in the other 10 Drosophila genomes
Summary
Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster), whereas putatively active sequences are present in others (D. simulans). Deletions may occur either by recombination, which is common to all classes of elements, or as a consequence of the transposition mechanism of the specific element concerned The latter occurs in LINE elements (Long Interspersed Nuclear Elements, known as non-LTR retrotransposons or retroposons), which are retroelements that use an RNA intermediate to transpose [2]. Considerable internal deletions have previously been reported in the inactive copies of several non-LTR retrotransposons [10], and this deletion mechanism seems to act at an high rate, since sequences that are similar at the nucleotide level may have very different internal deletions [10,11,18,19]
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