Drosophila Gene Research Articles

Gene model for the ortholog of Pten in Drosophila miranda.

Gene model for the ortholog of Phosphatase and tensin homolog ( Pten ) in the D. miranda Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2) Genome Assembly (GenBank Accession: GCA_000269505.2 ) of Drosophila miranda . This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Gene model for the ortholog of Myc in Drosophila eugracilis.

Gene model for the ortholog of Myc ( Myc ) in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of Drosophila eugracilis . This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.

High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here, we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution. We find that our contiguous genome assemblies allow characterization of chromosomal arrangements with ease and can facilitate analysis of inversion breakpoints. We also leverage a small panel of resequenced strains to explore the genomic pattern of divergence and polymorphism in this species and show that known demographic histories largely predicts the extent of genome-wide segregating polymorphism. We further find that a neo-X chromosome in Drosophila americana displays X-like levels of nucleotide diversity. We also found that unusual repetitive elements were responsible for much of the divergence in genome composition among species. Helitron-derived tandem repeats tripled in abundance on the Y chromosome in D. americana compared to Drosophila novamexicana, accounting for most of the difference in repeat content between these sister species. Repeats with characteristics of both transposable elements and satellite DNAs expanded by 3-fold, mostly in euchromatin, in both D. americana and D. novamexicana compared to D. virilis. Our results represent a major advance in our understanding of genome biology in this emerging model clade.

Biodiversity of Drosophila species at a new university campus in Kunshan, China

The project aimed to explore the biodiversity of Drosophila species in Kunshan using genomic approaches. DNA sequences, specifically the Cytochrome Oxidase I (COI) gene, were utilized as genetic "barcodes" to identify the organisms. Three wild-caught fruit flies and a D. melanogaster control were selected, and their DNA was isolated through PCR amplification of the COI gene. The PCR products were sequenced, and the results were used to create phylogenetic trees and uploaded to the Barcode of Life Database Student Data Portal (BOLD-SDP) alongside species photos. The results identified 10 Drosophila species, with 6 species remaining unchanged over two years and 3 new species discovered this year. One sample was identified as D. neohypocausta, a Chinese endemic species, which had appeared only in the last two years in Kunshan. However, its sample size was small, suggesting it may not be native to the area. Further research revealed significant genetic differentiation between different clades of D. immigrans, which likely explained the limited number of D. neohypocausta samples, as most D. immigrans species are confined to specific regions. To gain a comprehensive understanding of biogeographic, ecological, and evolutionary patterns across the Drosophila genus, expanded sampling and taxonomic revision are necessary, particularly for the large immigrans species groups that have been inferred as polyphyletic in some studies. This study underscores the importance of genomic approaches in taxon diagnosis and highlights the need for further exploration to uncover the intricate relationships within the Drosophila genus.

KYNURENINE PATHWAY INHIBITORS COMBINED WITH NAD+ PRECURSORS INCREASES LONGEVITY GENE EXPRESSION IN DROSOPHILA

Abstract With rates of aging-related functional decline rising, the need for novel intervention strategies to extend lifespan has increased. In humans, the kynurenine pathway (KP) metabolizes tryptophan and produces nicotinamide adenine dinucleotide (NAD+). KP is correlated negatively with longevity and increased KP metabolite concentrations decrease the average and maximum lifespans in flies. However, genetic and pharmacological inhibition of tryptophan metabolism and dietary supplementation of NAD+ precursors increase the average and maximum lifespans in flies. To comprehensively explore the effects of KP manipulation, we fed DGRP_229 Drosophila males diets infused with ⍺-MT (KP inhibitor), nicotinamide (NAM, an NAD+ precursor), or the combination of NAM and ⍺-MT. We found that all treatments resulted in increased average and maximum lifespans, with the combination treatment displaying the greatest increase compared to the control of 30% (P< 0.0001). The combination treatment resulted in an average lifespan increase of 15% in relation to ⍺-MT alone (P< 0.0001) and 18% in comparison to NAM alone (P< 0.0001). To gain more insight into the biological mechanisms through which different treatments affect lifespan, we performed qRT-PCR on 11 longevity genes in Drosophila. We found that the combination treatment significantly increased the expression of gigas (Gig) (P=0.03), which interacts with Tsc1 to control cellular growth by regulating insulin and TOR signaling pathways, and sirtuin 1 (Sirt1) (P=0.03), an NAD+-dependent histone deacetylase. Our results demonstrate that the combined treatment of KP inhibition and NAD+ precursor elicits a transcription response similar to other lifespan-enhancing treatments and could be used as an alternative intervention method.

Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures.

JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

Gene co-regulation caused by the special positional relationship in the early stages of Drosophila embryos

The genetic regulation mechanism of early Drosophila embryo has been a research hotspot in the past few decades. Understanding the early genetic regulation mechanisms of Drosophila embryos plays an important role in understanding the growth and development of other animals. In previous studies, an important Transcription Activator, Zelda (Zld), was reported. Zld is a global activator of early embryonic transcription. During the early development of embryos, all animals undergo the material-to-zygotic Transition (MZT), where Zld plays an important role in degrading maternal mRNA and mediating the expression of over 120 zygotic genes. The absence or mutation of Zld will directly lead to the inability of the embryo to complete the MZT process and result in lethality. TAGteam is a special sequence upstream of many genes in Drosophila, and Zld plays a role as a binding protein of TAGteam. TAGteam is a highly conserved sequence that generally exists in the form of CAGGTAG. Mutations or lack of TAGteam often result in inability to bind to Zld, resulting in the inability of genes to be expressed normally. The two genes involved in this experiment, CG14014 (2L: 5549709.. 550835 [-]) and CG18269 (2L: 5551838.. 5552756 [+]), are two adjacent genes on the Drosophila chromosome. They are located on two different DNA strands and facing in opposite directions, while their current role is not yet clear. There are typical TAGteam sequences upstream of both genes. This article conducts experiments to verify the relationship between these two genes and the regulation of Zld protein, and explores the possibility of their co-regulation by designing experiments.

Metaphase chromosomes of five Neotropical species of the genus Drosophila (Diptera, Drosophilidae).

The mitotic metaphases of five Andean species of genus Drosophila are described for the first time. The evolutionary and interspecific genetic relationships within three Neotropical Drosophila species groups are analyzed. The diploid chromosome number for each species is as follows: D.cashapamba Céspedes et Rafael, 2012 2n = 6 (2V, 1J) (X = J, Y = R), D.ecuatoriana Vela et Rafael, 2004 2n = 10 (3R, 2V) (X = V, Y = R), D.ninarumi Vela et Rafael, 2005 2n = 10 (3R, 1V, 1D) (X = V, Y = R), D.urcu Vela et Rafael, 2005 2n = 12 (4R, 2V) (X = V, Y = R), D.valenteae Llangarí-Arizo et Rafael, 2018 2n = 8 (3R, 1J) (X = J, Y = R).

Mask exhibits trxG-like behavior and associates with H3K27ac marked chromatin

The Trithorax group (trxG) proteins counteract the repressive effect of Polycomb group (PcG) complexes and maintain transcriptional memory of active states of key developmental genes. Although chromatin structure and modifications appear to play a fundamental role in this process, it is not clear how trxG prevents PcG-silencing and heritably maintains an active gene expression state. Here, we report a hitherto unknown role of Drosophila Multiple ankyrin repeats single KH domain (Mask), which emerged as one of the candidate trxG genes in our reverse genetic screen. The genome-wide binding profile of Mask correlates with known trxG binding sites across the Drosophila genome. In particular, the association of Mask at chromatin overlaps with CBP and H3K27ac, which are known hallmarks of actively transcribed genes by trxG. Importantly, Mask predominantly associates with actively transcribed genes in Drosophila. Depletion of Mask not only results in the downregulation of trxG targets but also correlates with diminished levels of H3K27ac. The fact that Mask positively regulates H3K27ac levels in flies was also found to be conserved in human cells. Strong suppression of Pc mutant phenotype by mutation in mask provides physiological relevance that Mask contributes to the anti-silencing effect of trxG, maintaining expression of key developmental genes. Since Mask is a downstream effector of multiple cell signaling pathways, we propose that Mask may connect cell signaling with chromatin mediated epigenetic cell memory governed by trxG.

A new species of the Drosophila tripunctata group (Diptera: Drosophilidae) associated with fallen flowers of six Lecythidaceae species in the Amazon Rainforest.

The tripunctata group falls under the subgenus Drosophila Falln, 1823 of the genus Drosophila Falln, 1823, and is composed of four subgroups and 17 species not assigned to subgroups. This group is widely distributed throughout tropical regions and is predominantly found in preserved forest environments. With a predicted high number of cryptic species, the occurrence of intraspecific morphological polymorphisms made it difficult to establish lines in the laboratory. The capture of males for comparison of the terminalia makes it hard to identify and delimit species; however, these difficulties can be overcome through the use of techniques such as searching for species in naturally occurring places, establishing isofemale lines in the laboratory, or using molecular techniques. In this work, we search for imagoes of species of the tripunctata group over present fallen flowers of the Lecythidaceae on the ground of the Amazon rainforest. The collected individuals were morphologically and molecularly analyzed. This species is described here under the binomial Drosophila lecythus sp. nov.

Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus.

The PIWI-interacting RNA (piRNA) pathway prevents endogenous genomic parasites, i.e. transposable elements, from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, are thought to define each species' piRNA repertoire and therefore its capacity to recognize and silence specific transposon families. The unistrand cluster flamenco (flam) is essential in the somatic compartment of the Drosophila ovary to restrict Gypsy-family transposons from infecting the neighbouring germ cells. Disruption of flam results in transposon de-repression and sterility, yet it remains unknown whether this silencing mechanism is present more widely. Here, we systematically characterise 119 Drosophila species and identify five additional flam-like clusters separated by up to 45 million years of evolution. Small RNA-sequencing validated these as bona-fide unistrand piRNA clusters expressed in somatic cells of the ovary, where they selectively target transposons of the Gypsy family. Together, our study provides compelling evidence of a widely conserved transposon silencing mechanism that co-evolved with virus-like Gypsy-family transposons.

Finding information about uncharacterized Drosophila melanogaster genes.

Genes that have been identified in the genome but remain uncharacterized with regards to function offer an opportunity to uncover novel biological information. Novelty is exciting but can also be a barrier. If nothing is known, how does one start planning and executing experiments? Here, we provide a recommended information-mining workflow and a corresponding guide to accessing information about uncharacterized Drosophila melanogaster genes, such as those assigned only a systematic coding gene identifier. The available information can provide insights into where and when the gene is expressed, what the function of the gene might be, whether there are similar genes in other species, whether there are known relationships to other genes, and whether any other features have already been determined. In addition, available information about relevant reagents can inspire and facilitate experimental studies. Altogether, mining available information can help prioritize genes for further study, as well as provide starting points for experimental assays and other analyses.

Evolution of secondary cell number and position in the Drosophila accessory gland.

In animals with internal fertilization, males transfer gametes and seminal fluid during copulation, both of which are required for successful reproduction. In Drosophila and other insects, seminal fluid is produced in the paired accessory gland (AG), the ejaculatory duct, and the ejaculatory bulb. The D. melanogaster AG has emerged as an important model system for this component of male reproductive biology. Seminal fluid proteins produced in the Drosophila AG are required for proper storage and use of sperm by the females, and are also critical for establishing and maintaining a suite of short- and long-term postcopulatory female physiological responses that promote reproductive success. The Drosophila AG is composed of two main cell types. The majority of AG cells, which are referred to as main cells, are responsible for production of many seminal fluid proteins. A minority of cells, about 4%, are referred to as secondary cells. These cells, which are restricted to the distal tip of the D. melanogaster AG, may play an especially important role in the maintenance of the long-term female post-mating response. Many studies of Drosophila AG evolution have suggested that the proteins produced in the gland evolve quickly, as does the transcriptome. Here, we investigate the evolution of secondary cell number and position in the AG in a collection of eight species spanning the entire history of the Drosophila genus. We document a heretofore underappreciated rapid evolutionary rate for both number and position of these specialized AG cells, raising several questions about the developmental, functional, and evolutionary significance of this variation.

PpGpp is present in, and functions to regulate sleep of, Drosophila

Sleep is essential for animals, and receives inputs from circadian, homeostasis, and environment, yet the mechanisms of sleep regulation remain elusive. Discovery of molecules in living systems and demonstration of their functional roles are pivotal in furthering our understanding of the molecular basis of biology. Here, we report that guanosine-5′-diphosphate, 3′-diphosphate (ppGpp) is present in Drosophila, and plays an important role in regulation of sleep and starvation-induced sleep loss (SISL). ppGpp is detected in germ-free Drosophila and hydrolyzed by an enzyme encoded by the mesh1 gene in Drosophila. Nighttime sleep and SISL were defected in mesh1 mutant flies, and rescued by expression of wildtype Mesh1, but not the enzymatically defective mutant Mesh1E66A. Ectopic expression of RelA, the Escherichia coli synthetase for ppGpp, phenocopied mesh1 knockout mutants, whereas overexpression of Mesh1 resulted in the opposite phenotypes, supporting that ppGpp is both necessary and sufficient in sleep regulation. A chemo connectomic screen followed by genetic intersection experiments implicates the Dilp2 neurons in the pars intercerebralis (PI) brain region as the site of ppGpp function. Our results have thus validated the presence of ppGpp in Drosophila and revealed a physiological role of ppGpp in sleep regulation for the first time.

Evolution at multiple processing levels underlies odor-guided behavior in the genus Drosophila

Olfaction is a fundamental sense guiding animals to their food. How the olfactory system evolves and influences behavior is still poorly understood. Here, we selected five drosophilid species, including Drosophila melanogaster, inhabiting different ecological niches to compare their olfactory systems at multiple levels. We first identified ecologically relevant natural food odorants from every species and established species-specific odorant preferences. To compare odor coding in sensory neurons, we analyzed the antennal lobe (AL) structure, generated glomerular atlases, and developed GCaMP transgenic lines for all species. Although subsets of glomeruli showed distinct tuning profiles, odorants inducing species-specific preferences were coded generally similarly. Species distantly related or occupying different habitats showed more evident differences in odor coding, and further analysis revealed that changes in olfactory receptor (OR) sequences partially explain these differences. Our results demonstrate that genetic distance in phylogeny and ecological niche occupancy are key determinants in the evolution of ORs, AL structures, odor coding, and behavior. Interestingly, changes in odor coding among species could not be explained by evolutionary changes at a single olfactory processing level but rather are a complex phenomenon based on changes at multiple levels.

Different Protein Groups Involved in Transcription Regulation in Development and Housekeeping Genes in Drosophila

Different Protein Groups Involved in Transcription Regulation in Development and Housekeeping Genes in Drosophila

Sedentary Behavior Impacts on the Epigenome and Transcriptome: Lessons from Muscle Inactivation in Drosophila Larvae.

The biological mechanisms linking sedentary lifestyles and metabolic derangements are incompletely understood. In this study, temporal muscle inactivation in Drosophila larvae carrying a temperature-sensitive mutation in the shibire (shi1) gene was induced to mimic sedentary behavior during early life and study its transcriptional outcome. Our findings indicated a significant change in the epigenetic profile, as well as the genomic profile, of RNA Pol II binding in the inactive muscles relative to control, within a relatively short time period. Whole-genome analysis of RNA-Pol II binding to DNA by muscle-specific targeted DamID (TaDa) protocol revealed that muscle inactivity altered Pol II binding in 121 out of 2010 genes (6%), with a three-fold enrichment of genes coding for lncRNAs. The suppressed protein-coding genes included genes associated with longevity, DNA repair, muscle function, and ubiquitin-dependent proteostasis. Moreover, inducing muscle inactivation exerted a multi-level impact upon chromatin modifications, triggering an altered epigenetic balance of active versus inactive marks. The downregulated genes in the inactive muscles included genes essential for muscle structure and function, carbohydrate metabolism, longevity, and others. Given the multiple analogous genes in Drosophila for many human genes, extrapolating our findings to humans may hold promise for establishing a molecular link between sedentary behavior and metabolic diseases.

Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.

Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.

Heterochromatic silencing of immune-related genes in glia is required for BBB integrity and normal lifespan in drosophila.

Glia and neurons face different challenges in aging and may engage different mechanisms to maintain their morphology and functionality. Here, we report that adult-onset downregulation of a Drosophila gene CG32529/GLAD led to shortened lifespan and age-dependent brain degeneration. This regulation exhibited cell type and subtype-specificity, involving mainly surface glia (comprising the BBB) and cortex glia (wrapping neuronal soma) in flies. In accordance, pan-glial knockdown of GLAD disrupted BBB integrity and the glial meshwork. GLAD expression in fly heads decreased with age, and the RNA-seq analysis revealed that the most affected transcriptional changes by RNAi-GLAD were associated with upregulation of immune-related genes. Furthermore, we conducted a series of lifespan rescue experiments and the results indicated that the profound upregulation of immune and related pathways was not the consequence but cause of the degenerative phenotypes of the RNAi-GLAD flies. Finally, we showed that GLAD encoded a heterochromatin-associating protein that bound to the promoters of an array of immune-related genes and kept them silenced during the cell cycle. Together, our findings demonstrate a previously unappreciated role of heterochromatic gene silencing in repressing immunity in fly glia, which is required for maintaining BBB and brain integrity as well as normal lifespan.

DrosOMA: the Drosophila Orthologous Matrix browser

Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.