For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Mating stimulates the rate of egg-laying by female insects. In Drosophila melanogaster this stimulation is initially caused by seminal fluid molecules transferred from the male (Acps or accessory gland proteins; reviewed in [1] [2] [3]). Egg-laying is a multi-step process. It begins with oocyte release by the ovaries, followed by egg movement down the oviducts and the deposition of eggs onto the substratum. Although two Acps are known to stimulate egg-laying [4] [5], they were detected by assays that do not discriminate between the steps of this process or allow examination of its earliest changes [4] [5] [6] [7]. To determine how egg-laying is regulated, we developed a generally applicable assay to separate the process into quantifiable steps, allowing us to assess the ovulation pattern and rate of egg movement. As the steps are interdependent yet potentially subject to independent controls, we determined the contribution of each step and effector independent of the others. We used a statistical method [8] [9] that separately considers and quantifies each 'path' to a common end. We found that the prohormone-like molecule Acp26Aa [5] [10] stimulates the first step in egg-laying - release of oocytes by the ovary. During mating, Acp26Aa begins to accumulate at the base of the ovaries, a position consistent with action on the ovarian musculature to mediate oocyte release. Understanding how individual Acps regulate egg-laying in fruitflies will help provide a full molecular picture of insects' prodigious fertility, of reproductive hormones, and of the roles of these rapidly evolving proteins [11] [12].

Male-derived accessory gland proteins that are transferred to females during mating have profound effects on female reproductive physiology including increased ovulation, mating inhibition, and effects on sperm utilization and storage. The extreme rates of evolution seen in accessory gland proteins may be driven by sperm competition and sexual conflict, processes that may ultimately drive complex interactions between female-and male-derived molecules and sperm. However, little is known of how gene expression in female reproductive tissues changes in response to the presence of male molecules and sperm. To characterize this response, we conducted parallel genomic and proteomic analyses of gene expression in the reproductive tract of 3-day-old unmated and mated female Drosophila melanogaster. Using DNA microarrays, we identified 539 transcripts that are differentially expressed in unmated vs. mated females and revealed a striking peak in differential expression at 6 h postmating and a marked shift from primarily down-regulated to primarily up-regulated transcripts within 3 h after mating. Combining two-dimensional gel electrophoresis and liquid chromatography mass spectrometry analyses, we identified 84 differentially expressed proteins at 3 h postmating, including proteins that appeared to undergo posttranslational modification. Together, our observations define transcriptional and translational response to mating within the female reproductive tract and suggest a bimodal model of postmating gene expression initially correlated with mating and the final stages of female reproductive tract maturation and later with the declining presence of male reproductive molecules and with sperm maintenance and utilization.accessory gland proteins ͉ reproduction ͉ reproductive tract ͉ sperm ͉ sexual conflict

Insects respond to crowding in a variety of ways that are usually exemplified by rapid changes in behavior and culminate in enduring long-term morphological and/or chromatic responses. A common feature of both short-term and long-term effects is that they are graded, dependent not only on density but also on the duration and on phase history of the maternal generation. Because of their exoskeletons, which are persistent for the duration of each instar and endure throughout adult life, overt changes in morphology or coloration are restricted to the molting period and shortly afterward, when cuticular hardening and pigmentation are expressed. Changes in internal organs or metabolism elicited by population density, being independent of integumental constraints, are not restricted to the molting period, but the temporal difference between internal and external responses is not of fundamental significance. Intraspecific responses to the presence of sibling insects are of apparent ecological significance and often involve directional movement and/or migration. They are mediated via the sensory system, involve signal transduction, and elicit downstream biochemical and physiological changes.

In animals with internal fertilization, ovulation and female sperm storage are essential steps in reproduction. While these events are often required for successful fertilization, they remain poorly understood at the developmental and molecular levels in many species. Ovulation involves the regulated release of oocytes from the ovary. Female sperm storage consists of the movement of sperm into, maintenance within, and release from specific regions of the female reproductive tract. Both ovulation and sperm storage elicit important changes in gametes: in oocytes, ovulation can trigger changes in the egg envelopes and the resumption of meiosis; for sperm, storage is a step in their transition from being "movers" to "fertilizers." Ovulation and sperm storage both consist of timed and directed cell movements within a morphologically and chemically complex environment (the female reproductive tract), culminating with gamete fusion. We review the processes of ovulation and sperm storage for Drosophila melanogaster, whose requirements for gamete maturation and sperm storage as well as powerful molecular genetics make it an excellent model organism for study of these processes. Within the female D. melanogaster, both processes are triggered by male factors during and after mating, including sperm and seminal fluid proteins. Therefore, an interplay of male and female factors coordinates the gametes for fertilization.

Mating triggers physiological and behavioral changes in females.To understand how females effect these changes, we used microarray, proteomic, and comparative analyses to characterize gene expression in oviducts of mated and unmated Drosophila females. The transition from non-egg laying to egg laying elicits a distinct molecular profile in the oviduct. Immune-related transcripts and proteins involved in muscle and polarized epithelial function increase, whereas cell growth and differentiation-related genes are down-regulated. Our combined results indicate that mating triggers molecular and biochemical changes that mediate progression from a ''poised'' state to a mature, functional stage.antimicrobial peptides ͉ network ͉ reproduction

Drosophila melanogaster mature oocytes in ovaries are arrested at metaphase I of meiosis. Eggs that have reached the uterus have released this arrest. It was not known where in the female reproductive tract egg activation occurs and what triggers it. We investigated when and where the egg is activated in Drosophila in vivo and at what meiotic stage the egg is fertilized. We found that changes in the egg's envelope's permeability, one feature of activation, initiate during ovulation, even while most of the egg is still within the ovary. The egg becomes impermeable as it proceeds down the oviducts; the process is complete by the time the egg is in the uterus. Cross-linking of vitelline membrane protein sV23 also increases progressively as the egg moves through the oviducts and the uterus. Activation also triggers meiosis to resume before the egg reaches the uterus, such that the earliest eggs that reach the uterus are in anaphase I. We discuss models for Drosophila egg activation in vivo.

Unlike vertically transmitted endosymbionts, which have broad effects on their host's germ line, the extracellular gut microbiota is transmitted horizontally and is not known to influence the germ line. Here we provide evidence supporting the influence of these gut bacteria on the germ line of Drosophila melanogaster. Removal of the gut bacteria represses oogenesis, expedites maternal-to-zygotic-transition in the offspring and unmasks hidden phenotypic variation in mutants. We further show that the main impact on oogenesis is linked to the lack of gut Acetobacter species, and we identify the Drosophila Aldehyde dehydrogenase (Aldh) gene as an apparent mediator of repressed oogenesis in Acetobacter-depleted flies. The finding of interactions between the gut microbiota and the germ line has implications for reproduction, developmental robustness and adaptation.