Vertical inheritance and bursts of transposition have shaped the evolution of the BS non-LTR retrotransposon in Drosophila

In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides

It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the Bithorax-complex (BX-C), which was one of the first genomic regions described to contain long non-coding RNAs in Drosophila. We showed that several altORFs could be predicted from coding and non-coding sequences of BX-C. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two Drosophila Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during Drosophila embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo.

Thermal sensitivity of the Spiroplasma-Drosophila hydei protective symbiosis: The best of climes, the worst of climes

The outcome of natural enemy attack in insects is commonly influenced by the presence of protective symbionts in the host. The degree to which protection functions in natural populations, however, will depend on the robustness of the phenotype and symbiosis to variation in the abiotic environment. We studied the impact of a key environmental parameter-temperature-on the efficacy of the protective effect of the symbiont Spiroplasma on its host Drosophila hydei, against attack by the parasitoid wasp Leptopilina heterotoma. In addition, we investigated the thermal sensitivity of the symbiont's vertical transmission, which may be a key determinant of the ability of the symbiont to persist. We found that vertical transmission was more robust than previously considered, with Spiroplasma being maintained at 25°C, at 18°C and with 18/15°C diurnal cycles, with rates of segregational loss only increasing at 15°C. Protection against wasp attack was ablated before symbiont transmission was lost, with the symbiont failing to rescue the fly host at 18°C. We conclude that the presence of a protective symbiosis in natural populations cannot be simply inferred from the presence of a symbiont whose protective capacity has been tested under narrow controlled conditions. More broadly, we argue that the thermal environment is likely to represent an important determinant of the evolutionary ecology of defensive symbioses in natural environments, potentially driving seasonal, latitudinal and altitudinal variation in symbiont frequency.

Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus

The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.

VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila

Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.

Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae

Hybridization between different genomes is a source of genomic instability, sometimes associated with transposable element (TE) mobilization. Previous work showed that hybridization between the species Drosophila buzzatii and Drosophila koepferae induced mobilization of different (TEs), the Osvaldo retrotransposon being the most unstable. However, we ignore the mechanisms involved in this transposition release in interspecific hybrids. In order to disentangle the mechanisms involved in this process, we performed Osvaldo expression studies in somatic and germinal tissues from hybrids and parental species. There was a trend towards increased Osvaldo expression in the somatic tissues of hybrid females and males, which was always significant in males compared to the parental species D. buzzatii but, not in females compared to maternal species D. koepferae. There were massive changes of Osvaldo expression in the testes, which varied depending on the hybrid generation and family. Moreover, Osvaldo hybridization signals, restricted to the apical and primary spermatocyte regions in parents, occupied broader region in the hybrids. In ovaries, there were no significant differences in Osvaldo expression rates between hybrids and the maternal species D. koepferae. The transcript location was restricted to ovarian nurse cells in both parents and hybrids, undetectable in some hybrids. This research highlights first, the existence of putative complex deregulation mechanisms different between sexes and cell types and second, disruption of Osvaldo activity particularly evident in testes from sterile hybrid males. Deeper studies of the total transcriptome in hybrids and parental species are necessary to gain a better knowledge of the TE deregulation pathways in hybrids.

A new genome-wide method to track horizontally transferred sequences: application to Drosophila

Because of methodological breakthroughs and the availability of an increasing amount of whole-genome sequence data, horizontal transfers (HTs) in eukaryotes have received much attention recently. Contrary to similar analyses in prokaryotes, most studies in eukaryotes usually investigate particular sequences corresponding to transposable elements (TEs), neglecting the other components of the genome. We present a new methodological framework for the genome-wide detection of all putative horizontally transferred sequences between two species that requires no prior knowledge of the transferred sequences. This method provides a broader picture of HTs in eukaryotes by fully exploiting complete-genome sequence data. In contrast to previous genome-wide approaches, we used a well-defined statistical framework to control for the number of false positives in the results, and we propose two new validation procedures to control for confounding factors. The first validation procedure relies on a comparative analysis with other species of the phylogeny to validate HTs for the nonrepeated sequences detected, whereas the second one built upon the study of the dynamics of the detected TEs. We applied our method to two closely related Drosophila species, Drosophila melanogaster and D. simulans, in which we discovered 10 new HTs in addition to all the HTs previously detected in different studies, which underscores our method’s high sensitivity and specificity. Our results favor the hypothesis of multiple independent HTs of TEs while unraveling a small portion of the network of HTs in the Drosophila phylogeny.

Specific activation of an I-like element in Drosophila interspecific hybrids

The non-long terminal repeat (LTR) retrotransposon I, which belongs to the I superfamily of non-LTR retrotransposons, is well known in Drosophila because it transposes at a high frequency in the female germline cells in I-R hybrid dysgenic crosses of Drosophila melanogaster. Here, we report the occurrence and the upregulation of an I-like element in the hybrids of two sister species belonging to the repleta group of the genus Drosophila, D. mojavensis, and D. arizonae. These two species display variable degrees of pre- and postzygotic isolation, depending on the geographic origin of the strains. We took advantage of these features to explore the transposable element (TE) dynamics in interspecific crosses. We fully characterized the copies of this TE family in the D. mojavensis genome and identified at least one complete copy. We showed that this element is transcriptionally active in the ovaries and testes of both species and in their hybrids. Moreover, we showed that this element is upregulated in hybrid males, which could be associated with the male-sterile phenotype.

Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals

Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79-99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite-host interaction might facilitate HTs.

The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats

Hybrid incompatibilities (HIs) cause reproductive isolation between species and thus contribute to speciation. Several HI genes encode adaptively evolving proteins that localize to or interact with heterochromatin, suggesting that HIs may result from co-evolution with rapidly evolving heterochromatic DNA. Little is known, however, about the intraspecific function of these HI genes, the specific sequences they interact with, or the evolutionary forces that drive their divergence. The genes Hmr and Lhr genetically interact to cause hybrid lethality between Drosophila melanogaster and D. simulans, yet mutations in both genes are viable. Here, we report that Hmr and Lhr encode proteins that form a heterochromatic complex with Heterochromatin Protein 1 (HP1a). Using RNA-Seq analyses we discovered that Hmr and Lhr are required to repress transcripts from satellite DNAs and many families of transposable elements (TEs). By comparing Hmr and Lhr function between D. melanogaster and D. simulans we identify several satellite DNAs and TEs that are differentially regulated between the species. Hmr and Lhr mutations also cause massive overexpression of telomeric TEs and significant telomere lengthening. Hmr and Lhr therefore regulate three types of heterochromatic sequences that are responsible for the significant differences in genome size and structure between D. melanogaster and D. simulans and have high potential to cause genetic conflicts with host fitness. We further find that many TEs are overexpressed in hybrids but that those specifically mis-expressed in lethal hybrids do not closely correlate with Hmr function. Our results therefore argue that adaptive divergence of heterochromatin proteins in response to repetitive DNAs is an important underlying force driving the evolution of hybrid incompatibility genes, but that hybrid lethality likely results from novel epistatic genetic interactions that are distinct to the hybrid background.

Sister species capable of mating often produce hybrids that are sterile or die during development. This reproductive isolation is caused by incompatibilities between the two sister species' genomes. Some hybrid incompatibilities involve genes that encode rapidly evolving proteins that localize to heterochromatin. Heterochromatin is largely made up of highly repetitive transposable elements and satellite DNAs. It has been hypothesized that rapid changes in heterochromatic DNA drives the changes in these HI genes and thus the evolution of reproductive isolation. In support of this model, we show that two rapidly evolving HI proteins, Lhr and Hmr, which reproductively isolate the fruit fly sister species D. melanogaster and D. simulans, repress transposable elements and satellite DNAs. These proteins also help regulate the length of the atypical Drosophila telomeres, which are themselves made of domesticated transposable elements. Our data suggest that these proteins are part of the adaptive machinery that allows the host to respond to changes and increases in heterochromatin and to maintain the activity of genes located within or adjacent to heterochromatin.

Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis

In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.