Biology subjects

Burlet, N.

Publications and source records attributed to Burlet, N..

7 recordsLinked to original sources

bioRxiv2025

Exploring the role of transposable elements to sex gap in longevity in Drosophila species

In Drosophila, like in many other animal species, females tend to live longer than males, a phenomenon known as sex gap in longevity (SGL). One possible explanation for this phenomenon could be related to the activity of transposable elements (TE), which may be present at higher levels in the heterogametic sex. TE activity is normally repressed by epigenetic mechanisms, but this regulation weakens with age. Sex chromosomes, such as the Y chromosome, are enriched in TEs, and age-related TE activity may therefore be more pronounced in older males than in older females, likely affecting longevity patterns. Using three Drosophila species, we show that SGL varies naturally among wild-type populations, reflecting both intra-and inter-species differences. Transcriptomic data revealed increased age-related TE expression in D. melanogaster and D. suzukii flies, but not in D. simulans. Moreover, we observed a higher number of upregulated TE copies in older males compared to older females across all the three species tested. Additionally, we detected an increase in TE-chimeric transcript generation in some aged samples, particularly in D. suzukii males. Finally, the replacement of the Y chromosome between strains with different SGL led to a progressive reduction in male lifespan and increased TE transcriptional release over generations, suggesting a Y chromosome important role in male longevity. Our work highlights the importance of investigating the role of TEs to better understand differences in longevity between sexes and across different species.

genomics↗

bioRxiv2024

Relaxed purifying selection is associated with an accumulation of transposable elements in flies

Although the mechanisms driving the evolution of genome size are not yet fully understood, one potentially important factor is the dynamics of the accumulation of mobile selfish genetic elements called transposable elements (TEs). Since most of these sequences are neutral or slightly deleterious, a negative correlation between genome size and selection efficacy is expected. However, previous studies based on empirical data from closely related species with contrasting life history traits (thought to result in contrasting levels of selection efficacy) have yielded inconsistent results, leaving this issue controversial. In this study, we perform the first large-scale analysis of the effect of drift on genome size evolution, without any prior assumption about the amount of drift in each sampled species. We reconstructed a phylogeny based on whole-genome data (2,242 genes) for 77 Drosophilid species to examine correlations between genome size, TE content, and measures of selection efficacy (especially using dN/dS ratios of non-synonymous to synonymous divergence). We highlight a strong phylogenetic inertia in genome size and confirm that TEs are the major components of genome size. Using an integrative approach that controls for shared history, we find that genome-wide dN/dS are strongly positively correlated with genome size and TE content, particularly in GC-poor genes. This study highlights the critical importance of controlling for heterogeneity in base composition when testing the controversial correlation between evolutionary rates and genome size. Furthermore, our review of previous studies reveals that the absence of evidence for TE accumulation in association with increased genetic drift may be attributed to a secondary effect of changes in life history traits on TE dynamics. In conclusion, this work provides evidence for TE proliferation in fly genomes when purifying selection is reduced and genetic drift increases, shedding new light on the role of transposable elements and genetic drift in the evolution of genome architecture.

evolutionary biology↗

bioRxiv2023

Community structure of heritable viruses in a Drosophila-parasitoids complex

The diversity and phenotypic impacts related to the presence of heritable bacteria in insects have been extensively studied in the last decades. On the contrary, heritable viruses have been overlooked for several reasons, including technical ones. This is regrettable because of the size of this gap knowledge and because case study indicate that viruses may have profound impact on the functionning of individuals and communities. Additionally, the factors that may shape viral communities are poorly known, except in some very specific viral-insect systems. Here we analyze the community structure of heritable viruses in a multi-hosts-multi-parasitoids community. Drosophilidae and their larval and pupal parasitoids were sampled in two locations, two years and two seasons. After two lab generations, putative DNA and RNA viruses were purified and sequenced. Our analysis revealed the presence of 53 viruses (including 37 new viruses), the great majority of which were RNA viruses. The "species" factor was by far the most significant one, explaining more than 50% of the variance in viral structure. Additionally, parasitoids had a higher number of heritable viruses compared to their hosts, suggesting that this lifestyle favours the association with viruses. Finally, our community-level survey challenged previous interpretation concerning the host range of some previously described viruses.

evolutionary biology↗

bioRxiv2023

A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH)

Odysseus (OdsH) was the first gene described in Drosophila related to speciation and hybrid sterility. This gene was first described in the melanogaster subgroup and more specifically in the sterile hybrids from crosses between D. mauritiana and D. simulans. Its origin is attributed to the duplication of the gene unc-4, which would have occurred in the ancestor of the subgenus Sophophora. By using a much larger sample of Drosophila species, we showed that contrary to what has been previously proposed, OdsH origin occurred approximately 62 million years ago (Mya). Then, OdsH have experienced rapid neofunctionalization in male reproductive tracts, evidenced by its evolutionary rates, expression and transcription factor binding sites. Furthermore, the analysis of the OdsH peptide sequence allowed the identification of mutations in the DNA- and protein-binding domains of D. mauritiana that could result in incompatibility with genomes from other species. We then explored the expression of OdsH in the spermatocytes of D. arizonae and D. mojavensis, a pair of recently diverged sister species with incomplete reproductive isolation and expected to find the involvement of OdsH in hybrid sterility. Our data indicated that OdsH expression is not atypical in male-sterile hybrids from these species. In conclusion, we have demonstrated that the origin of OdsH occurred earlier than previously proposed and that its neofunctionalization in male sexual functions occurred rapidly after its origin. Our results also suggested that its role as a speciation gene, as in the melanogaster subgroup of species, may be restricted to this specific taxon.

evolutionary biology↗

bioRxiv2023

Detection and identification of transposable element transcripts using Long Read RNA-seq in Drosophila germline tissues

Transposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs can disrupt nearby genes by donating their intrinsic regulatory sequences, for instance, promoting the ectopic expression of a cellular gene. TE transcription is therefore not only necessary for TE transposition per se but can also be associated with TE-gene fusion transcripts, and in some cases, be the product of pervasive transcription. Hence, correctly determining the transcription state of a TE copy is essential to apprehend the impact of the TE in the host genome. Methods to identify and quantify TE transcription have mostly relied on short RNA-seq reads to estimate TE expression at the family level while using specific algorithms to discriminate copy-specific transcription. However, assigning short reads to their correct genomic location, and genomic feature is not trivial. Here we retrieved full-length cDNA (TeloPrime, Lexogen) of Drosophila melanogaster gonads and sequenced them using Oxford Nanopore Technologies. We show that long-read RNA-seq can be used to identify and quantify transcribed TEs at the copy level. In particular, TE insertions overlapping annotated genes are better estimated using long reads than short reads. Nevertheless, long TE transcripts (> 4.5 kb) are not well captured. Most expressed TE insertions correspond to copies that have lost their ability to transpose, and within a family, only a few copies are indeed expressed. Long-read sequencing also allowed the identification of spliced transcripts for around 107 TE copies. Overall, this first comparison of TEs between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.

bioinformatics↗

bioRxiv2021

Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

Transposable elements (TEs) are middle-repeated DNA sequences that can move along chromosomes using internal coding and regulatory regions. By their ability to move and because they are repeated, TEs can promote mutations. Especially they can alter the expression pattern of neighboring genes and have been shown to be involved in the mammalian regulatory network evolution. Human and mouse share more than 95% of their genomes and are affected by comparable diseases, which makes the mouse a perfect model in cancer research. However not much investigation concerning the mouse TE content has been made on this topics. In human cancer condition, a global activation of TEs can been observed which may ask the question of their impact on neighboring gene functioning. In this work, we used RNA sequences of highly aggressive pancreatic tumors from mouse to analyze the gene and TE deregulation happening in this condition compared to pancreas from healthy animals. Our results show that several TE families are deregulated and that the presence of TEs is associated with the expression divergence of genes in the tumor condition. These results illustrate the potential role of TEs in the global deregulation at work in the cancer cells.

genomics↗

bioRxiv2021

The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

genomics↗