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Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae.
Mol Biol Evol. 2005 Jan; 22(1):29-39.MB

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. 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 overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.

Authors+Show Affiliations

Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Spain.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15356275

Citation

Tubío, Jose Manuel C., et al. "Structural and Evolutionary Analyses of the Ty3/gypsy Group of LTR Retrotransposons in the Genome of Anopheles Gambiae." Molecular Biology and Evolution, vol. 22, no. 1, 2005, pp. 29-39.
Tubío JM, Naveira H, Costas J. Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol. 2005;22(1):29-39.
Tubío, J. M., Naveira, H., & Costas, J. (2005). Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Molecular Biology and Evolution, 22(1), 29-39.
Tubío JM, Naveira H, Costas J. Structural and Evolutionary Analyses of the Ty3/gypsy Group of LTR Retrotransposons in the Genome of Anopheles Gambiae. Mol Biol Evol. 2005;22(1):29-39. PubMed PMID: 15356275.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. AU - Tubío,Jose Manuel C, AU - Naveira,Horacio, AU - Costas,Javier, Y1 - 2004/09/08/ PY - 2004/9/10/pubmed PY - 2005/5/20/medline PY - 2004/9/10/entrez SP - 29 EP - 39 JF - Molecular biology and evolution JO - Mol Biol Evol VL - 22 IS - 1 N2 - 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. 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 overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/15356275/Structural_and_evolutionary_analyses_of_the_Ty3/gypsy_group_of_LTR_retrotransposons_in_the_genome_of_Anopheles_gambiae_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msh251 DB - PRIME DP - Unbound Medicine ER -