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Genes are important in defining genetic variability, but they do not constitute the largest component of genomes, which in most organisms contain large amounts of various repeated sequences including transposable elements (TEs), which have been shown to account for most of the genome size. TEs contribute to genetic diversity by their mutational potential as a result of their ability to insert into genes or gene regulator regions, to promote chromosomal rearrangements, and to interfere with gene networks. Also, TEs may be activated by environmental stresses (such as temperature or radiation) that interfere with epigenetic regulation systems, and makes them powerful mutation agents in nature. To understand the relationship between genotype and phenotype, we need to analyze the portions of the genome corresponding to TEs in great detail, and to decipher their relationships with the genes. For this purpose, we carried out comparative analyses of various natural populations of the closely-related species Drosophila melanogaster and Drosophila simulans, which differ with regard to their TE amounts as well as their ecology and population size., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Transposable elements (TEs) are indwelling components of genomes, and their dynamics have been a driving force in genome evolution. Although we now have more information concerning their amounts and characteristics in various organisms, we still have little data from overall comparisons of their sequences in very closely-related species. While the Drosophila melanogaster genome has been extensively studied, we have only limited knowledge regarding the precise TE sequences in the genomes of the related species Drosophila simulans, Drosophila sechellia and Drosophila yakuba. In this study we analyzed the number and structure of TE copies in the sequenced genomes of these four species. Our findings show that, unexpectedly, the number of TE insertions in D. simulans is greater than that in D. melanogaster, but that most of the copies in D. simulans are degraded and in small fragments, as in D. sechellia and D. yakuba. This suggests that all three species were invaded by numerous TEs a long time ago, but have since regulated their activity, as the present TE copies are degraded, with very few full-length elements. In contrast, in D. melanogaster, a recent activation of TEs has resulted in a large number of almost-identical TE copies. We have detected variants of some TEs in D. simulans and D. sechellia, that are almost identical to the reference TE sequences in D. melanogaster, suggesting that D. melanogaster has recently been invaded by active TE variants from the other species. Our results indicate that the three species D. simulans, D. sechellia, and D. yakuba seem to be at a different stage of their TE life cycle when compared to D. melanogaster. Moreover, we show that D. melanogaster has been invaded by active TE variants for several TE families likely to come from D. simulans or the ancestor of D. simulans and D. sechellia. The numerous horizontal transfer events implied to explain these results could indicate introgression events between these species., (Copyright © 2010 Elsevier B.V. All rights reserved.)

Background: Transposable elements (TEs) are major players in evolution. We know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in their amplification and elimination from genomes and populations. Taking advantage of differences in the amount and distribution of the Long Interspersed Nuclear Element (LINE), helena in Drosophila melanogaster and D. simulans, we analyzed the DNA sequences of copies of this element in samples of various natural populations of these two species., Results: In situ hybridization experiments revealed that helena is absent from the chromosome arms of D. melanogaster, while it is present in the chromosome arms of D. simulans, which is an unusual feature for a TE in these species. Molecular analyses showed that the helena sequences detected in D. melanogaster were all deleted copies, which diverged from the canonical element. Natural populations of D. simulans have several copies, a few of them full-length, but most of them internally deleted., Conclusion: Overall, our data suggest that a mechanism that induces internal deletions in the helena sequences is active in the D. simulans genome.

Tirant is a long terminal repeat (LTR) retrotransposon with an average of 11 insertion sites on the chromosome arms of Drosophila melanogaster flies collected from natural populations worldwide. In the sibling species Drosophila simulans, tirant is found only in African populations, which harbor a few insertion sites (1 to 5) on the chromosome arms, although some tirant sequences are present in the heterochromatin of most populations. This distribution in D. simulans reflects either the recent genomic invasion of African populations by a new variant of tirant, or a loss of tirant from the entire species apart from some sequence relics still present in Africa. In an attempt to clarify the situation, we focused on the LTR-UTR region of tirant copies from various populations of both D. melanogaster and D. simulans. We found two distinct types of regulatory region: one type was present in both D. melanogaster and D. simulans, and the other was present only in D. simulans. Copies of this latter type of tirant were transcriptionally inactive in gonads. Here we propose that the present day distribution of tirant in D. simulans populations reflects an ancient invasion of D. simulans by tirant copies followed by the loss of active copies from most populations, apart from the African ones, suggesting that this loss is still ongoing in this species.

Transposable elements (TEs) in the two sibling species, Drosophila melanogaster and D. simulans, differ considerably in amount and dynamics, with D. simulans having a smaller amount of TEs than D. melanogaster. Several hypotheses have been proposed to explain these differences, based on the evolutionary history of the two species, and claim differences either in the effective size of the population or in genome characteristics. Recent data suggest, however, that the higher amount of TEs in D. melanogaster could be associated with the worldwide invasion of D. melanogaster a long time ago while D. simulans is still under the process of such geographical spread. Stresses due to new environmental conditions and crosses between migrating populations could explain the mobilization of TEs while the flies colonize. Colonization and TE mobilization may be strong evolutionary forces that have shaped and are still shaping the eukaryote genomes.

Transposable elements (TEs), which promote various kinds of mutations, constitute a large fraction of the genome. How they invade natural populations and species is therefore of fundamental importance for understanding the dynamics of genetic diversity and genome composition. On the basis of 85 samples of natural populations of Drosophila simulans, we report the distributions of the genome insertion site numbers of nine TEs that were chosen because they have a low average number of sites. Most populations were found to have 0-3 insertion sites, but some of them had a significantly higher number of sites for a given TE. The populations located in regions outside Africa had the highest number of sites for all elements except HMS Beagle and Coral, suggesting a recent increase in the activity of some TEs associated with the colonization patterns of Drosophila simulans. The element Tirant had a very distinctive pattern of distribution: it was identified mainly in populations from East Africa and some islands in the Indian Ocean, and its insertion site number was low in all these populations. The data suggest that the genome of the entire species of Drosophila simulans may be being invaded by TEs from populations in which they are present in high copy number.

We compared the codon usage of sequences of transposable elements (TEs) with that of host genes from the species Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens. Factorial correspondence analysis showed that, regardless of the base composition of the genome, the TEs differed from the genes of their host species by their AT-richness. In all species, the percentage of A + T on the third codon position of the TEs was higher than that on the first codon position and lower than that in the noncoding DNA of the genomes. This indicates that the codon choice is not simply the outcome of mutational bias but is also subject to selection constraints. A tendency toward higher A + T on the third position than on the first position was also found in the host genes of A. thaliana, C. elegans, and S. cerevisiae but not in those of D. melanogaster and H. sapiens. This strongly suggests that the AT choice is a host-independent characteristic common to all TEs. The codon usage of TEs generally appeared to be different from the mean of the host genes. In the AT-rich genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Saccharomyces cerevisiae, the codon usage bias of TEs was similar to that of weakly expressed genes. In the GC-rich genome of D. melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest that selection acts on TEs and that TEs may display specific behavior within the host genomes. [ABSTRACT FROM AUTHOR]

Males of three inbred lines of Drosophila melanogaster were heat-shocked 90 min at 37°C. The progenies from treated and untreated males mated with untreated females of the same line were checked for their chromosomal insertion patterns of various mobile elements by either in situ hybridization or Southern blots. No modification in the pattern of insertion of the elements studied was observed after heat treatment. Hence, heating males of our inbred lines did not mobilize mobile elements, contrary to recent reports on other lines of Drosophila melanogaster. [ABSTRACT FROM AUTHOR]

Abstract: Transposable elements, which are major components of most genomes, are known to accumulate in heterochromatic regions in which they have progressively diverged in sequence by mutations and internal deletions and insertions (indels) during the course of evolution. They therefore provide a record of the genomic events that have shaped the genomes, some of which could correspond to speciation events. Using the sequence divergence between the long terminal repeats (LTRs), we estimated the date of the insertion events of the LTR retrotransposon copies embedded within the heterochromatin regions of the Drosophila melanogaster genome. We did not detect traces of any specific waves of mobilization of retrotransposons within heterochromatin, apart from a very recent wave, which corresponds to the numerous LTR retrotransposon copies found in euchromatin. [Copyright &y& Elsevier]