Multiple invasions of Errantivirus in the genus Drosophila

Abstract

Aiming to contribute to the knowledge of the evolutionary history of Errantivirus, a phylogenetic analysis of the env gene sequences of Errantivirus gypsy, gtwin, gypsy2, gypsy3, gypsy4 and gypsy6 was carried out in 33 Drosophilidae species. Most sequences were obtained from in silico searches in the Drosophila genomes. The complex evolutionary pattern reported by other authors for the gypsy retroelement was also observed in the present study, including vertical transmission, ancestral polymorphism, stochastic loss and horizontal transfer. Moreover, the elements gypsy2, gypsy3, gypsy4 and gypsy6 were shown to have followed an evolutionary model that is similar to gypsy. Fifteen new possible cases of horizontal transfer were suggested. The infectious potential of these elements may help elucidate the evolutionary scenario described in the present study.

hosimary: a new hAT transposon group involved in horizontal transfer

“…Hence, the same rate of TE and host gene dS should be expected when we comparing two species. However, when a TE is horizontally transmitted the pairwise comparison between the species presented a significantly lower dS value for the TE as compared to the dS observed for host gene (Silva and Kidwell 2000;Ludwig et al 2008;Bartolomé et al 2009). Considering that the dS values are inversely correlated with the codon bias usage (Sharp and Li 1989), the level of codon bias presented by the host gene can influence the inference of horizontal transfer events.…”

“…In this case, to avoid under-and over-estimation of horizontal transfer events, we took into consideration the level of codon bias presented by the TE and the genes (Ludwig et al 2008). The codon bias usage was calculated in the DnaSP 4.0 software (Rozas et al 2003) by the codon bias index (CBI; Morton 1993) and the effective number of codons (Nc; Wright 1990).…”

Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus

“…Some of the transfers are relatively recent, e.g., those occurring between D. melanogaster and D. erecta (Gypsy S1: 0-3.1 Mya) and between D. erecta and D. yakuba (Gypsy6: 0.562 Mya). 44 However, the HTs can also have occurred in more distant times, e.g., those occurring between D. erecta and D. melanogaster (Gypsy S2: 2.5-3.9 Mya) and between D. erecta and Z. tuberculatus (Gypsy S2: 5.2-11.2 Mya). 15 However, the fact that Gypsy produces viral particles does not exclude the possibility of other modes of transmission, such as transmission by vectors or even sexual transmission via introgressive hybridization.…”

“…One noteworthy approach is to analyze the TE rate of the synonymous substitution (Ks or Ds) and that of nuclear genes. [14][15][16][41][42][43][44][45][46][47] This approach allows the HT event to be dated using the rationale that if the TEs are evolving vertically and the lack of congruence in the phylogeny is a consequence of differential subfamily distribution in the species analyzed, the Ks values of the TE sequences and those of the nuclear gene(s) should be equivalent. However, if the Ks of the TE are significantly lower than that of the nuclear gene, the lower Ks values can be explained by a small divergence time of the TE copies between the species as a consequence of HT.…”

New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies

“…In this case, indels relative to the canonical P sequence of D. melanogaster were removed to conserve the open reading frames of some sequences, whereas stop codons were considered as missing information. The amethyldopa (amd), alcohol dehydrogenase (adh), and/or amyrel (amy) nuclear genes were used in dS comparisons to test for horizontal transfer (using one-tailed Fisher's exact tests; Ludwig et al 2008). R scripts (R Development Core Team 2011) were used to conduct multiple dS tests.…”