Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

The Evolution of SINEs and LINEs in the genus Chironomus (Diptera)

Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.

Distribution of the bilbo non-LTR retrotransposon in Drosophilidae and its evolution in the Drosophila obscura species group

The bilbo element is a non-LTR retrotransposon isolated from Drosophila subobscura. We conducted a distribution survey by Southern blot for 52 species of the family Drosophilidae, mainly from the obscura and melanogaster groups. Most of the analyzed species bear sequences homologous to bilbo from D. subobscura. In the obscura group, species from the same species subgroup also share similar Southern blot patterns. To investigate the phylogenetic relationship among these elements, we analyzed eight copies of a short sequence of the element from several species of the obscura group. The obtained phylogram agrees with the phylogeny of the species, which suggests vertical transmission of the element.

Identification of Waldo-A and Waldo-B, two closely related non-LTR retrotransposons in Drosophila

We have identified two novel, closely related subfamilies of non-long-terminal-repeat (non-LTR) retrotransposons in Drosophila melanogaster, the Waldo-A and Waldo-B subfamilies, that are in the same lineage as site-specific LTR retrotransposons of the R1 clade. Both contain potentially active copies with two large open reading frames, having coding capacities for a nucleoprotein as well as endonuclease and reverse transcriptase activities. Many copies are truncated at the 5' end, and most are surrounded by target site duplications of variable lengths. Elements of both subfamilies have a nonrandom distribution in the genome, often being inserted within or very close to (CA)(n) arrays. At the DNA level, the longest elements of Waldo-A and Waldo-B are 69% identical on their entire length, except for the 5' untranslated regions, which have a mosaic organization, suggesting that one arose from the other following new promoter acquisition. This event occurred before the speciation of the D. melanogaster subgroup of species, since both Waldo-A and Waldo-B coexist in other species of this subgroup.

Gypsy group retrotransposon Tv1 from Drosophila virilis

We have determined the nucleotide sequence of the 6868 bp full-size retrotransposon termed 'Tv1'. Tv1 was isolated from the DNA fraction of extracellular virus-like particles of Drosophila virilis culture cells. Tv1 has the typical structure for a gypsy-group retrotransposon. The Tv1 element was found to be flanked by 453 bp long terminal direct repeats identical to each other. The central part of the element contains three long open reading frames which resemble the gag, pol and env genes of retroviruses. ORF2 includes conservative motifs of protease, reverse transcriptase, RNase H and integrase in the order characteristic for the gypsy-group retrotransposons. Although most copies of Tv1 are located in pericentromeric heterochromatin, the amplification of this family demonstrated in the cell culture and site polymorphism observed in different Drosophila strains suggest functional activity of the Tv1 element.

Molecular identification of the active ninja retrotransposon and the inactive aurora element in Drosophila simulans and D. melanogaster

How transposable elements evolve is a key facet in understanding of spontaneous mutation and genomic rearrangements in various organisms. One of the best ways to approach this question is to study a newly evolved transposable element whose presence is restricted to a specific population or strain. The retrotransposons ninja and aurora may provide insights into the process of their evolution, because of their contrasting characteristics, even though they show high sequence identity. The ninja retrotransposon was found in a Drosophila simulans strain in high copy number and is potent in transposition. On the other hand, aurora elements are distributed widely among the species belonging to the Drosophila melanogaster species complex, but are immobile at least in D. melanogaster. In order to distinguish the two closely resembled retrotransposons by molecular means, we determined and compared DNA sequence of the elements, and identified characteristic internal deletions and nucleotide substitutions in 5'-long terminal repeats (LTR). Analyses of the structure of ninja homologs and LTR sequences amplified from both genomic and cloned DNA revealed that the actively transposable ninja elements were present only in D. simulans strains, but inactive aurora elements exist in both D. melanogaster and D. simulans.