DrosoPhyla: genomic resources for drosophilid phylogeny and systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4000 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the groups and genera in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred well-supported group and species trees for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Macrozoobenthos assemblage patterns in European carp (Cyprinus carpio) ponds − the importance of emersed macrophyte beds

Qualitative and quantitative differences in benthic macrozoobenthos distribution in carp pond littoral zones (macrophyte areas; LM) and pelagic zones (macrophyte-free areas; MF) were assessed in four commercial carp (Cyprinus carpio) grow-out ponds in the Czech Republic (semi-intensive management) and Austria (organic management) monthly over the growing season (June-September) of 2016 and 2017. While differences in environmental parameters and granulometric composition between LM and MF were statistically non-significant (p > 0.05), organic matter content was significantly higher (p < 0.05) in LM. Average macrozoobenthos density and biomass in LM (mean 431 ind.m−2 and 6.78 g.m−2) was usually significantly higher (p > 0.05) than MF (371 ind.m−2 and 3.17 g.m−2). A similar trend was observed for zoobenthos diversity, with LM having a higher diversity (76 taxa) than MF (47 taxa). At the start of the growing season, chironomid density was higher (p < 0.05) in muddy MF zones, regardless of management type, while oligochaete density was higher in muddy LM. The density of both groups later declined, such that density was significantly higher (p > 0.05) in sandy substrates, regardless of habitat or management type. Our data suggest a significant drop in macrozoobenthos density and biomass compared with historical data, mainly due to new management techniques (fertilisation, supplementary feeding) and intensification (higher stock densities), suggesting that pond management is crucial as regards benthic invertebrate development and diversity. Our results indicate that emersed LM beds positively influence macrozoobenthos performance in carp ponds, potentially making them biodiversity hotspots. Further, LM beds can be regarded as invertebrate harbours, and hence should be protected and encouraged.

Characterizing the transcriptional expression and in situ localization of the Dnmt2 gene in Drosophila willistoni

Background: Organisms that have only the DNA methyltransferase 2 (Dnmt2) to mediate the DNA methylation are called "Dnmt2-only" and they have been investigated in recent surveys. Drosophila is one of the “Dnmt2-only” organisms and is also an ideal model for Dnmt2 research. However, the biological function of the Dnmt2 protein is still uncertain. Some studies have pointed to a putative role during the early stages of invertebrate development. In this work, we present our findings on the Dnmt2 expression in D. willistoni, a neotropical species of large ecological versatility and peculiar molecular features. Results: By RT-PCR and in situ hybridization we demonstrate here the presence of transcripts not only in the early stages of development, but also during the oogenesis. Using qPCR analysis, we verify that Dnmt2 transcription level is higher during early stages of development, though transcription levels are subtly higher in D. willistoni adults than in D. melanogaster levels found in previous studies. We also mapped the Dnmt2 on the IIL chromosome arm (Muller’s B element) of D. willistoni, near at the end of the singular telomeric region. Conclusions: Our findings give insights on the possible biological function of Dnmt2-related processes associated with the development and differentiation of oocytes since germinative tissue formation seems to require a higher expression of Dnmt2. The Dnmt2 localization in the subtelomeric region brings up a series of issues that involve the peculiar characteristics of D. willistoni Dnmt2 enzyme, like evolutionary patterns and the epigenetic phenomena of sex-specific methylation.

From individual Wnt pathways towards a Wnt signalling network

Wnt proteins play important roles during vertebrate and invertebrate development. They obviously have the ability to activate different intracellular signalling pathways. Based on the characteristic intracellular mediators used, these are commonly described as the Wnt/β-catenin, the Wnt/calcium and the Wnt/Jun N-terminal kinase pathways (also called planar cell polarity pathway). In the past, these different signalling events were mainly described as individual and independent signalling branches. Here, we discuss the possibility that Wnt proteins activate a complex intracellular signalling network rather than individual pathways and suggest a graph representation of this network. Furthermore, we discuss different ways of how to predict the specific outcome of an activation of this network in a particular cell type, which will require the use of mathematical models. We point out that the use of deterministic approaches via the application of differential equations is suitable to model only small aspects of the whole network and that more qualitative approaches are possibly a suitable starting point for the prediction of the global behaviour of such large protein interaction networks.

rasp, a putative transmembrane acyltransferase, is required for Hedgehog signaling

Members of the Hedgehog (Hh) family encode secreted molecules that act as potent organizers during vertebrate and invertebrate development. Post-translational modification regulates both the range and efficacy of Hh protein. One such modification is the acylation of the N-terminal cysteine of Hh. In a screen for zygotic lethal mutations associated with maternal effects, we have identified rasp, a novel Drosophila segment polarity gene. Analysis of the rasp mutant phenotype, in both the embryo and wing imaginal disc demonstrates that rasp does not disrupt Wnt/Wingless signaling but is specifically required for Hh signaling. The requirement of rasp is restricted only to those cells that produce Hh; hh transcription, protein levels and distribution are not affected by the loss of rasp. Molecular analysis reveals that rasp encodes a multipass transmembrane protein that has homology to a family of membrane bound O-acyl transferases. Our results suggest that Rasp-dependent acylation is necessary to generate a fully active Hh protein.