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Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species

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Abstract

LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.

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Acknowledgments

This work was supported by grants from FAPERGS (0411965) and CNPq. We thank CNPq for fellowships. We thank Agencourt Bioscience Corporation, the Broad Institute, J. Craig Venter Institute, and Washington University School of Medicine Genome Sequencing Center for prepublication access to the genome sequence data. We are grateful to Dr. Henrique Bunselmeyer Ferreira, Dr. Paulo Marcos Pinto, Dr. Lizandra Jaqueline Robe, Dr. Christian Macagnan Probst, MSc. Nina Roth Mota and MSc. Paloma Rubin for the valuable help during the realization of this work. We also thank Dr. K. Yoshida for kindly providing the pXTom2 plasmid; Dr. Damon Lish for statistical test discussion; Dr. Vera Lúcia da Silva Valente, Dr. Marco Silva Gottschalk, Dr. Jean David for providing several Drosophila strains; and two anonymous reviewers for their helpful suggestions on the manuscript.

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  1. Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, 91501-970, Brazil

    Newton Medeiros Vidal, Adriana Ludwig & Elgion Lucio Silva Loreto

  2. Departamento de Biologia, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, Brazil

    Elgion Lucio Silva Loreto

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  1. Newton Medeiros Vidal
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Correspondence to Elgion Lucio Silva Loreto.

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Communicated by T. Clandinin.

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Analysis of Drosophila species distribution (DOC 549 kb)

Table S1 Strains used for dot blot and PCR screenings with the respective results (DOC 149 kb)

Table S2 List of the collapsed sequences in the phylogenies and their corresponding representative sequence (DOC 45 kb)

Table S3 Accession numbers for amd, cdc6, sod and adh genes (DOC 45 kb)

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Vidal, N.M., Ludwig, A. & Loreto, E.L.S. Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species. Mol Genet Genomics 282, 351–362 (2009). https://doi.org/10.1007/s00438-009-0468-0

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