title: Polymorphism of canonical and noncanonical gypsy sequences in different species of Drosophila melanogaster subgroup: possible evolutionary relations.
abstract: Mobile genetic elements constitute a substantial part of eukaryotic genome and play an important role in its organization and functioning. Co-evolution of retrotransposons and their hosts resulted in the establishment of control systems employing mechanisms of RNA interference that seem to be impossible to evade. However, "active" copies of endogenous retrovirus gypsy escape cellular control in some cases, while its evolutionary elder "inactive" variants do not. To clarify the evolutionary relationship between "active" and "inactive" gypsy we combined two approaches: the analysis of gypsy sequences, isolated from G32 Drosophila melanogaster strain and from different Drosophila species of the melanogaster subgroup, as well as the study of databases, available on the Internet. No signs of "intermediate" (between "active" and "inactive") gypsy form were found in GenBank, and four full-size G32 gypsy copies demonstrated a convergence that presumably involves gene conversion. No "active" gypsy were revealed among PCR generated gypsy ORF3 sequences from the various Drosophila species indicating that "active" gypsy appeared in some population of D. melanogaster and then started to spread out. Analysis of sequences flanking gypsy variants in G32 revealed their predominantly heterochromatic location. Discrepancy between the structure of actual gypsy sites in G32 and corresponding sequences in database might indicate significant inter-strain heterochromatin diversity.
authors.affiliation: V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov street, 119991 Moscow, Russian Federation. ben.salenko@gmail.com
authors.forename: Veniamin B
authors.initials: VB
authors.lastname: Salenko
authors.forename: Alina P
authors.initials: AP
authors.lastname: Kotnova
authors.forename: Nina N
authors.initials: NN
authors.lastname: Karpova
authors.forename: Natalia V
authors.initials: NV
authors.lastname: Lyubomirskaya
authors.forename: Yuriy V
authors.initials: YV
authors.lastname: Ilyin
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D020077:Endogenous Retroviruses / Q000235:genetics*; D015723:Gene Library; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D018626:Retroelements / Q000235:genetics / Q000502:physiology; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D018626:Retroelements