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MBE Advance Access published online on September 8, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh251
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 30, 2004

Research Article

Structural and Evolutionary Analyses of the Ty3/gypsy Group of LTR Retrotransposons in the Genome of Anopheles gambiae

Jose Manuel C. Tubío 1, Horacio Naveira 2, and Javier Costas 3

1 Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Spain
2 Departamento de Bioloxía Celular e Molecular, Universidade de A Coruña, Spain
3 Unidade de Medicina Molecular, INGO, Complexo Hospitalario Universitario de Santiago de Compostela, Spain


  Abstract

The recent availability of the genome of Anopheles gambiae offers an extraordinary opportunity for comparative studies of the diversity of transposable elements (TEs) and their evolutionary dynamics between two related species, taking advantage of the existing information from Drosophila melanogaster. To this goal, we screened the genome of A. gambiae for elements belonging to the Ty3/gypsy group of long terminal repeat (LTR) retrotransposons. The A. gambiae genome displays a rich diversity of LTR retrotransposons, clearly greater than D. melanogaster. We have characterized in detail 63 families, belonging to five of the nine main lineages of the Ty3/gypsy group. The Mag lineage is the most diverse and abundant, with more than 30 families. In sharp contrast with this finding, a single family belonging to this lineage has been found in D. melanogaster, here reported for the first time in the literature, most probably consisting of old inactive elements. The CsRn1 lineage is also abundant in A. gambiae but almost absent from D. melanogaster. And, conversely, the Osvaldo lineage has been detected in Drosophila but not in Anopheles. Comparison of structural characteristics of different families led to the identification of several lineage-specific features such as the primer binding site (PBS), the gag-pol translational recoding signal (TRS), which is extraordinarily diverse within the Ty3/gypsy retrotransposons of A. gambiae, or the presence/absence of specific amino acid motifs. Interestingly, some of these characteristics, although in general well conserved within lineages, may have evolved independently in particular branches of the phylogenetic tree. We also show evidence of recent activity for around 75% of the families. Nevertheless, almost all families contain a high proportion of degenerate members and solitary LTRs (solo-LTRs), indicative of a lower turnover rate of retrotransposons belonging to the Ty3/gypsy group in A. gambiae than in D. melanogaster. Finally, we have detected significant over-representations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.

Keywords: Ty3/gypsy; retrotransposon; Anopheles gambiae; Drosophila melanogaster.
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