2008). . . 1995). Patterns of speciation in Drosophila revisited. Molecular genetic aspects of sex determination in Drosophila. 2000), is the nematode Caenorhabditis elegans. sechellia and D. simulansspecies that differ in ecology and life history characteristics despite diverging just 240,000 years ago (Garrigan et al. The black arrows show the direction of sister chromatid separation during the completion of mitotic division. . Stark A, Lin M F, Kheradpour P, Pedersen J S, Parts L et al. Tissues within a larva that, during metamorphosis, will undergo dramatic changes to become a particular adult structure like an eye, wing, or leg. . 2008). Chiang A S, Lin C Y, Chuang C C, Chang H M, Hsieh C H et al. Genomic organization of the Drosophila telomere retrotransposable elements. The new animal phylogeny: reliability and implications. Around 15,000 years ago, D. melanogaster migrated from its ancestral range in southern Sub-Saharan Africa to Europe and subsequently colonized much of the rest of the world, reaching the Americas in just the last few hundred years (David and Capy 1988; Lachaise et al. Finally, after establishing identity within each segment, the homeotic selector genes (also called HOX genes) control the specification of tissues or organs in particular segments (Lewis 1978). What genes mediate basic cell biological events within specific cell types? 2008). Drosophila brain structure and function develop and age significantly from larval to adult stage. Accurate genetic crosses are enabled by visible marker mutations that allow selection of offspring that inherited one version or the other of a chromosome. 2002). High-throughput RNA interference screens in Drosophila tissue culture cells. . Transfection frequency in S2 cells is fairly high, making transgene analysis relatively straightforward (e.g., for immunoprecipitation or subcellular localization or proteins). . Drosophila 12 Genomes Consortium et al., 2007Evolution of genes and genomes on the Drosophila phylogeny. True cellularization occurs in stage 5, followed by gastrulation (stage 8), which determines the three germ layers. 2014) combined with phenotypes assayed from the same lines are an unprecedented resource for genome-wide association studies (GWAS) (Ober et al. In some wing cells, the FLP recombinase triggers recombination between FRT sites on nonsister chromatids, and (C) one copy each of the GFP marker and the mutation of interest will switch between homologous chromosomes. Manipulation of an innate escape response in Drosophila: photoexcitation of acj6 neurons induces the escape response. Nolte V, Pandey R V, Kofler R, Schlotterer C. Noor M A, Grams K L, Bertucci L A, Reiland J. Ober U, Ayroles J F, Stone E A, Richards S, Zhu D et al. 2002). 2012). As we begin the second century of using Drosophila as an experimental tool in the fields of genetics, cell biology, developmental biology, neurobiology, and evolutionary biology, the groundwork laid during the first century will enable the tractable complexity of the fly to continue offering valuable insights into basic science as well as applied, translational research toward human health. The key innovations that allow us to answer these questions are P-element-mediated transformation as well as the Gal4/UAS bipartite expression system. The genetics of speciation at the diploid level. . Annotation IDs in other Drosophila species are identified by a different prefix (e.g., GA for D. pseudoobscura IDs and GD for D. simulans IDs). Single male offspring from this cross are outcrossed again, and male and female siblings within these individual lines are then crossed to start inbred lines that propagate different founding mutations. In contrast, nanos localizes to the posterior and regulates abdominal segment formation (Gavis and Lehmann 1992). The chromosomes of Drosophila melanogaster Methods Mol Biol. Jonathan Weiners book Time, Love, Memory covers Benzers important contributions in detail and in a compelling way (Weiner 1999). Stages of embryonic development. Work over the past decade on the olfactory system in the fly has mapped neural connections associated with response to individual odorants. A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. These are further examples of the creative naming of D. melanogaster gene mutations based on the phenotypes they express. The first FLP transgenic flies had the gene under the control of the hsp70 promoter to permit the induction of the FLP and thus recombination at specific time points during development with an increase of temperature (Golic and Lindquist 1989). Humans are largely responsible for D. melanogaster migration in recent history, probably through the trade of fruit (David and Capy 1988; Markow and OGrady 2007). The latest version of DPGP (DPGP3; http://www.dpgp.org/dpgp3/DPGP3.html) involves the sequencing of >300 individuals from a single population in Zambia, in what is presumed to be the ancestral range of the species (Pool et al. Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. 3: RESEARCH0080. D. High-throughput RNAi screening in cultured cells: a users guide. The genetics are designed such that the desired recombination also removes the Gal80 repressor, allowing reporter gene expression to be activated only in cells where recombination has occurred. In the lab, researchers have developed ways to use TEs as tools for mutagenesis and transformation (see A Drosophila Genetic Toolkit below). Unpredictable expression levels can add uncertainty regarding whether a rescue experiment, or other manipulations, are working as designed. What is now known as the DobzhanskyMuller model of speciation is the basis of many contemporary studies of speciation genetics (e.g., Coyne and Orr 1989, 1997). A powerful gene editing system, used in many organisms and contexts, that enables the generation of mutations in specific genes through targeting the Cas9 endonuclease to a desired DNA region with a complementary guide RNA.. Philos. The first assembly was published in 2000 (Adams et al. Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. Ryder E, Blows F, Ashburner M, Bautista-Llacer R, Coulson D et al. A few examples of online resources with more narrow foci are described below, listed according to the questions they help address. . Population genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. (B) Different mutations occur in each cell of the feeding flies, including sperm (indicated by pink, yellow, and green sperm cells). The 21st century thus far has seen development of new targeted gene knock-down and knock-out approaches using RNA interference and the CRISPR/Cas9 system, the latter of which is quickly and dramatically expanding in popularity and use (Gratz et al. Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. Another Fly Room accomplishment involved polytene chromosomes, which consist of many replicated but not separated DNA molecules adhering in register; these are easily stained and visualized, with each chromosome showing a unique banding pattern. E-mail: Search for other works by this author on: The genome sequence of Drosophila melanogaster. 2007). The Chromosomes of Drosophila melanogaster | SpringerLink Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Out of these ideas came much of what we understand about evolution today, including that populations evolve by natural selection acting on genetic variation. Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. 2010). Drosophilists also pioneered surveys of molecular genetic variation, first using protein electrophoresis to study allozyme variation (Lewontin and Hubby 1966) and then DNA sequence polymorphism (Kreitman 1983). FlyAtlas2, http://flyatlas.gla.ac.uk/flyatlas/index.html, catalogs gene expression at the level of mRNA enrichment across multiple tissues for most genes, based on microarray data (Chintapalli et al. The most recent Nobel Prize for work using D. melanogaster was awarded to Jules Hoffman in 2011 for his 1996 work on the innate immune response. The art and design of genetic screens: Drosophila melanogaster. Sex-specific isoforms of Dsx and Fru then mediate expression of downstream effectors that govern sexual morphology and behavior (Baker et al. 2009). 2003; Frankel et al. As with other model systems, the fly community has used chemical mutagens such as ethyl methane sulfonate (EMS) added to fly food or ionizing radiation such as X-rays to trigger everything from single base pair mutations to larger chromosomal changes (Greenspan 1997). Cytological analysis suggests that the bulk of the fourth, including the portion that appears banded in the polytene chromosomes, is heterochromatic; the banded region includes blocks of middle repetitious DNA associated with heterochromatin protein 1 (HP1). Typically accomplished using a modified FLP/FRT protocol that incorporates the dominant female sterile ovoD (ensures that only females where recombination occurred in the germline can lay eggs). The hardwiring of development: organization and function of genomic regulatory systems. Mature eggs leave the ovaries and travel through the oviduct, during which time some of the stored sperm are released. Success is often dependent on how efficiently a particular phenotype can be observed. Sucena E, Delon I, Jones I, Payre F, Stern D L. Thibault S T, Singer M A, Miyazaki W Y, Milash B, Dompe N A et al. In addition, work in cell culture suggested that the inverted repeat could produce off-target effects where multiple genes expression was altered by the system (Perrimon and Mathey-Prevot 2007). As in most insects, adult structures in fruit flies arise from imaginal cells that are fated during embryogenesis. A second approach is to clone small enhancer regions from genes of interest to create GAL4 expression lines that replicate the expression pattern of that gene. These engineered chromosomes with visible markers and multiple inversions are called balancer chromosomes. Balancer chromosomes have a third feature as wellrecessive lethal mutationsto prevent mutations of interest from being selected out of an inbred population. Daniels S B, Peterson K R, Strausbaugh L D, Kidwell M G, Chovnick A. Davis T R, Wickham T J, McKenna K A, Granados R R, Shuler M L et al. Single nucleotide changes in acetylcholinesterase (Ace) cause resistance to organophosphates and carbamates (Mutero et al. While the sperm entry site determines anterior/posterior polarity in some organisms such as C. elegans, this polarity is already specified in fly eggs before fertilization. Together, these species span a wide range of ecological habitats, life history characteristics, and evolutionary divergence times (Singh et al. For beginning researchers, the Interactive Fly, http://www.sdbonline.org/sites/fly/aimain/1aahome.htm, is a good starting point for exploring the roles of genes in developmental processes. Gametogenesis in flies has served as a useful system to study stem cell specification and maintenance (Matunis et al. 2007). FlyBase, http://flybase.org, (St Pierre et al. Morgan ultimately became known as the founder of Drosophila geneticsall current Drosophila researchers can trace their intellectual pedigree back to Morgan. 1984; Zehring et al. The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. The second sequenced Drosophila genome was D. pseudoobscura, a species with historical importance in evolutionary genetics (Richards et al. In males, the absence of early Sxl expression results in default processing of Sxl and tra transcripts that contain an early stop codon. 1987); however, a Drosophila cell line of true epithelial origin has yet to be derived. Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. The goal of a forward genetic screen is to identify genes involved in a particular developmental process, biochemical activity, or behavior, with no a priori model of which genes might be important. A large scale collaborative project to define functional elements in the genomes of Drosophila and the nematode C. elegans. . 2007). Thus, XO mammals are females, with ovaries, a uterus, and oviducts (but usually very few, if any, ova). Recently, the complete molecular structures of several commonly used balancers were determined by whole-genome sequencing. Gene names and abbreviations are italicized but usually not capitalized, unless the allele for which they are named is dominant to wild type. Genome data and annotations available via FlyBase continue to be refined and updated by the Berkeley Drosophila Genome Project (BDGP), http://www.fruitfly.org/ (e.g., Hoskins et al. This innovation has created a significant step forward in resolution, allowing for the examination and genetic manipulation of single mutant neurons within the adult brain to determine which neurons and which genes affect certain behaviors. Avoids the difficulties of position affect variation associated with random insertions as integration sites can be selected that are known to express well. The development of egg cells in females (oogenesis) and sperm cells in males (spermatogenesis) involves not only the reductional chromosomal divisions of meiosis but also dramatic cellular reorganization and shape changes. His book Genetics and the Origin of Species (Dobzhansky 1937) was crucial in the formulation of the Modern Synthesis, which connected genetics with other areas to create a broad understanding of the mechanism of evolution. 2014) (Figure 3B). 1984). Not all TEs cause problems in the genome; rather, some TEs now serve an important biological role. . The molecular evolutionary basis of species formation. (C) Outcrossing the mutagenized flies to untreated females yields (D) offspring that each potentially have a different new mutations throughout their bodies, indicated schematically by body colors corresponding to the sperm cells above. 2007). Thus, the more complex nervous system of the brain has become more tractable with each passing decade. In flies heterozygous for that mutation but with FRTs on both homologous chromosomes, FLP-triggered mitotic recombination would lead to patches of homozygous mutant cells, typically identified by a linked recessive marker or loss of a linked fluorescent gene product. A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. Commonly known as fruit or vinegar flies, they are often found on rotting fruit or other decaying matter (Powell 1997). Upon fertilization, embryogenesis is completed in 24 hr, followed by three larval stages (termed first, second, and third instar) with a molting event at each stage transition. Neofunctionalization of young duplicate genes in Drosophila. . The chromosomes of Drosophila melanogaster. . 2012; Lack et al. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the flys tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. Genome Biol. . Where is a certain gene expressed in the fly during development and/or later in the adult? DnaSP, DNA polymorphism analyses by the coalescent and other methods. In addition, a more sophisticated system has been built, mosaic analysis with a repressible cell marker (MARCM), to allow for the analysis of individually marked mutant cells in an unlabeled heterozygous background (Lee and Luo 2001). The references for each genome are as follows: (1) Hu et al. Images adapted from the Atlas of Drosophila Development (Hartenstein 1993) and used with permission. GAL4 system in Drosophila: a fly geneticists Swiss army knife. 1993; Ikonomou et al. The small genome size and longtime use as a model organism made D. melanogaster an appealing candidate genome to use as a proof of principle for whole genome shotgun sequencing and assembling of larger, more complex genomes (Adams et al. Wilson C, Pearson R K, Bellen H J, OKane C J, Grossniklaus U et al. Genome-wide association study of sleep in Drosophila melanogaster. Around day 5, third instar larvae crawl out of the food to pupate on the side of the vial. The ommatidium is composed of eight photoreceptor cells, with photoreceptors 16 positioned radially and photoreceptors 7 and 8 in the middle (with R7 positioned above R8). (A) Organization of the Drosophila melanogaster genome. They belong to the Droso-philidae family; and are most frequently known as fruit flies or often called vinegar, wine or pomace flies. Genetic analysis of the fruit fly has helped the neuroscience community understand all levels of neural function from the development of a nervous system, neuronal function and plasticity at the molecular level, adult neural networks, and the neurobiology of complex behaviors (Bellen et al. The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo. 2007), 120 Mb of which is euchromatin (Adams et al. 2010), proboscis extension (Gordon and Scott 2009), nocioception (Hwang et al. Seances Acad. A second approach to creating genome-wide libraries to examine gene function has been the development of RNA interference in both transgenic animals and cell lines. In some cases, adult homozygotes are not viable (as in the yellow population) and so researchers interested in earlier developmental steps may examine embryos and larvae within these populations to find dying homozygotes. Schmidt J M, Good R T, Appleton B, Sherrard J, Raymant G C et al. Generalized scheme for a forward genetic screen using chemical mutagenesis. Some early optogenetic work was done in the fly to address a variety of behavioral circuits including odorant learning and responses (Bellmann et al. To remedy this unpredictability, a new transformation system was developed using the serine recombinase protein from the PhiC31 bacteriophage, which recombines sequences using the attB and attP site-specific DNA sequences (Groth et al. Chiu J C, Jiang X, Zhao L, Hamm C A, Cridland J M et al. Life cycle of D. melanogaster. Can controlled expression of a particular gene (or variants thereof) in developmental time and cellular location help elucidate that genes function? This seminal work on the nature and origin of mutations earned Muller a Nobel Prize in 1946 and set the stage for scientists to generate (using radiation, and, later, chemicals) vast collections of mutant strains for dissecting the biology of many processes. While gene knock-out technology was more difficult to achieve in flies than in other model systems, Kent Golics group developed such techniques around the turn of the 21st century (Rong and Golic 2000, 2001). Transposition of cloned P elements into Drosophila germ line chromosomes. 1986), the efforts to map connectomes of more complicated adult nervous systems is being aided by the genetic and cell biological reagents available in the fly. A protein complex network of Drosophila melanogaster. [10] Sperm competition and sperm preference have thus been observed based on the genetics of both the male and female. Sapiro A L, Ihry R J, Buhr D L, Konieczko K M, Ives S M et al. 1982; Engels 1983; Kidwell 1983)! (B) Transgenic flies carrying either of the two constructs alone (top) do not express the gene of interest, but when crossed into the same fly, the tissue-specific promoter (a wing promoter in this example) drives expression of GAL4, which turns on the gene of interest (here indicated by green) in the specified tissue. 2005) and adaptive evolution (e.g., the McDonaldKreitman test (McDonald and Kreitman 1991), and the HudsonKreitmanAguade test (Hudson et al. 2000). . The most distant relative to D. melanogaster is the Hawaiian picture wing species D. grimshawi. (G) Researchers then test homozygous flies (darker pink and green) for the phenotype of interest. Sperm transfer, storage, displacement, and utilization in Drosophila melanogaster. Work is underway to identify specific genes regulated by sex-specific isoforms of Fru (Neville et al. The original versions of this system placed FRT recombination sites on all of the arms of the D. melanogaster chromosomes to enable mitotic recombination between homologous chromosomes in the presence of the FLP recombinase. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. The subsequent molecular cloning of the D. melanogaster period gene in 1984 led to identification of the transcriptional feedback loop of period/timeless and a continually growing set of interconnected pathways that play a role in behavioral rhythms (Bargiello et al. After 10 synchronized rounds of division, nuclei migrate to the periphery where they become partially encapsulated by actin-based furrow canals (stage 3/4). Similar cell-shape changes drive anterior and posterior midgut invaginations of cells fated to become the endoderm. It is therefore possible to find gynandromorphs, in which part of the fly body has male characteristics and other parts female (for example, due to loss of one X chromosome in some cells within an otherwise XX female).