GenesSequencesFlyBaseGeneticsEuchromatic portionTranscriptomeEukaryotic genomesAnnotationGenomicBiologyArabidopsisGenePhylogenetic2002Sequence of the humanSpeciesNovoPredictionConsortiumAnalysesFliesChromosomalTranscriptionAssemblyModelSequencingClonesLineageSimilaritiesProteinsMetabolicResearchersPestBacterialHumanDataAnalysisSizeEvolutionaryFeaturesStudyControlFactors
Genes21
- Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. (biomedcentral.com)
- The fraction of transcription factor genes among all genes is slightly higher in Arabidopsis (5.9%) compared with Drosophila , C. elegans and yeast (4.5, 3.5 and 3.5%, respectively). (biomedcentral.com)
- Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
- However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
- Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. (inrae.fr)
- The current coverage is, however, sufficient for the Human Genome Project to enter a new phase, in which the entire sequence can be analyzed to identify genes, regulatory regions and other genomic elements and structures. (biomedcentral.com)
- Both pufferfish genomes encode five tenascin genes: two tenascin-C paralogs, a tenascin-R with domain organization identical to mammalian and avian tenascin-R, a small tenascin-X with previously undescribed GK repeats, and a tenascin-W. Four tenascin genes corresponding to tenascin-C, tenascin-R, tenascin-X and tenascin-W were also identified in the X. tropicalis genome. (biomedcentral.com)
- The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. (nyu.edu)
- The UCLA Minor in Biomedical Research is excited to announce a publication in the journal G3: Genes Genomes Genetics, reporting data collected by 245 UCLA undergraduates and 31 high school students, all of whom are coauthors of the work. (ucla.edu)
- For this publication, students used the fruit fly, Drosophila melanogaster , to see which genes were expressed within the different cell types, and how this changed over the course of development. (ucla.edu)
- In completing this work, students examined the gene expression patterns of greater than five hundred genes, analyzing over 50,000 microscopic images. (ucla.edu)
- In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits. (flybase.org)
- Systematic identification of tRNA genes in Drosophila melanogaster. (flybase.org)
- While the transcription of innate immunity genes in response to bacterial infection has been well-characterised in the Drosophila model, we recently demonstrated the capacity for such transcription to evolve in flies selected for improved antibacterial defense. (biomedcentral.com)
- By spelling out protein-coding genes in the genome and comparing the house fly sequence to that of the fruit fly, Drosophila melanogaster , the team has endeavored to unravel genetic factors coinciding with house fly features. (genomeweb.com)
- For example, the M. domestica genome housed almost 150 cytochrome P450 enzyme-coding genes, consistent with a potentially bolstered detoxification system in the house fly. (genomeweb.com)
- Using these DNA and RNA sequences, the team put together - and annotated - a 691 million base assembly that spans more than three-quarters of the fly's complete genome sequence and contains an estimated 14,810 protein-coding genes. (genomeweb.com)
- While most of those resembled genes described in Drosophila , some 1,934 genes appeared to be specific to the house fly lineage. (genomeweb.com)
- The house fly genome contained sequences for some 771 apparent immune-related genes, for example, including 355 that are not homologous to Drosophila immune genes. (genomeweb.com)
- Consistent with their role as scent-based waste scavengers, the house flies had higher-than-usual representation by chemoreceptor and odorant-related genes in their genome, authors of the study noted. (genomeweb.com)
- Only two Bcl-2 family genes have been found in Drosophila melanogaster including the pro-cell survival, human Bok-related orthologue, Buffy. (sdbonline.org)
Sequences10
- Complete annotations as well as the members and sequences of the 62 groups reported are available for download. (uni-hamburg.de)
- Flybase BLAST -Searches all Drosophila reads and provides links to the individual matched sequences through the NCBI. (bcm.edu)
- With the completed genome sequences of Saccharomyces cerevisiae (budding yeast), Caenorhabditis elegans and Drosophila melanogaster , complete proteomes from representatives of three eukaryotic kingdoms (plants, fungi and animals) are now available for comprehensive comparative studies. (biomedcentral.com)
- These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. (inrae.fr)
- Genome sequences for most metazoans and plants are incomplete because of the presence of repeated DNA in the heterochromatin. (inrae.fr)
- The phylogenetic interactions among gypsy sequences from Drosophila types is not end up being often coincident with those of their hosts, that could end up being indicative of horizontal transfer during evolutionary background [6,7,9,10]. (healthyguide.info)
- One way to judge the potential influence from the gypsy infectious capability in the evolutionary background of gypsy sequences from Drosophila , is certainly to investigate the infective capability of gypsy homologous sequences from types apart from D. melanogaster . (healthyguide.info)
- Debate and Outcomes Sequences homologous to gypsy from D. melanogaster are distributed among Drosophila types. (healthyguide.info)
- This was achieved by looking genomes for the current presence of full-length env coding sequences and evaluating their efficiency. (healthyguide.info)
- In addition, we sequenced the full genome of a leucistic individual and obtained a highly-contiguous near-chromosome quality assembly of 1.69 Gb with an N50 of 14.5 Mb and an L50 of 29 sequences. (unige.ch)
FlyBase3
- In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
- The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. (flybase.org)
- FlyBase: updates to the Drosophila melanogaster knowledge base. (flybase.org)
Genetics2
- Starting with Charles W. Woodworth's 1901 proposal of the use of this species as a model organism, D. melanogaster continues to be widely used for biological research in genetics, physiology, microbial pathogenesis, and life history evolution. (wikipedia.org)
- D. melanogaster is typically used in research owing to its rapid life cycle, relatively simple genetics with only four pairs of chromosomes, and large number of offspring per generation. (wikipedia.org)
Euchromatic portion2
- In a collaborative effort with the Berkeley Drosophila Genome Project (BDGP) and Celera Genomics , we have mapped and sequenced the euchromatic portion of the Drosophila melanogaster genome. (bcm.edu)
- As of late 2000, the public human sequence was primarily based on approximately 24,000 accessioned bacterial artificial chromosome (BAC) clones covering 97% of the euchromatic portion of the genome [ 6 ]. (biomedcentral.com)
Transcriptome3
- Comparative validation of the D. melanogaster modENCODE transcriptome annotation. (bcm.edu)
- Phylogenomic analyses have been made possible by the dramatically decreasing costs of genome/transcriptome sequencing of non-model organisms [ 8 ]. (biomedcentral.com)
- In order to generate these comprehensive phylogenomic data sets, several cost-effective alternatives to whole genome or transcriptome sequencing have been proposed. (biomedcentral.com)
Eukaryotic genomes2
- LTR retrotransposons and endogenous retroviruses (ERVs) are transposable elements in eukaryotic genomes well suited for computational identification. (uni-hamburg.de)
- A comparative study based on four fully sequenced eukaryotic genomes has revealed profound differences in the sets of transcription factors used by plants, fungi and animals. (biomedcentral.com)
Annotation3
- We also performed an example annotation and classification of LTR retrotransposon insertions in the Drosophila melanogaster 5.8 genome as a proof of concept. (uni-hamburg.de)
- However, the challenges in genome annotation remain daunting [ 10 ], and the research community can anticipate years of additional work and manual curation to produce a true gene map of high quality. (biomedcentral.com)
- Functional annotation of the genome is primarily hampered by the lack of a unified transcript index. (biomedcentral.com)
Genomic2
- The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. (biomedcentral.com)
- As they reported online today in Genome Biology , the researchers pooled genomic DNA from half a dozen female house flies, using it as a template to generate sequence reads that were then assembled into a 691 million base M. domestica genome. (genomeweb.com)
Biology1
- The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, and genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest," corresponding author Jeffrey Scott, an entomology researcher at Cornell University, and his colleagues wrote. (genomeweb.com)
Arabidopsis2
- The recent completion of the Arabidopsis thaliana genome sequence allowed the first prediction of a full plant proteome. (biomedcentral.com)
- Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. (biomedcentral.com)
Gene10
- Comparisons with true aphids (for which complete genomes have been sequenced) should also allow to link differences in life-traits of the two groups with changes in gene repertoires or shifts in patterns of expression. (biomedcentral.com)
- We report here a functionally annotated human gene index placed directly on the genome. (biomedcentral.com)
- genome, and get away the control exerted with the flamenco gene normally, whose item represses flexibility[4]. (healthyguide.info)
- Furthermore, in D. melanogaster perform the gypsy components have an entire useful env gene [10]. (healthyguide.info)
- A single tenascin gene was identified in the genome of C. intestinalis that encodes a polypeptide with domain features common to all vertebrate tenascins. (biomedcentral.com)
- The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis. (flybase.org)
- Automated generation of gene summaries at the Alliance of Genome Resources. (flybase.org)
- Using a candidate-gene approach, we then identify in the leucistic genome a single-nucleotide deletion that generates a frameshift and a premature termination codon in the melanocyte inducing transcription factor (MITF) gene. (unige.ch)
- Here, we demonstrate that the unique Drosophila eya gene is also involved in the response specific to DNA. (cnrs.fr)
- The directed expression of alpha-synuclein , a gene contributing to inherited forms of Parkinson disease (PD), in the dopaminergic neurons (DA) of flies provides a robust model of PD complete with the loss of neurons and accompanying motor defects. (sdbonline.org)
Phylogenetic3
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. (inrae.fr)
- Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. (biomedcentral.com)
- However, for many phylogenetic questions, a dense, comprehensive sampling of genomes/transcriptomes is a still prohibitively expensive enterprise. (biomedcentral.com)
20022
- Release of the drosophila sequence was in 2002 ( link ). (bcm.edu)
- My subjective list would have included the malaria genome paper (MJ Gardner et al, Nature 2002) - TB and malaria are the two greatest infectious disease killers of humans - but it came in at #12 using citation criteria. (fieldofscience.com)
Sequence of the human1
- The sequence of the human nuclear genome has been completed in draft form by an international public consortium consisting of 16 sequencing centers and associated computational facilities [ 1 ]. (biomedcentral.com)
Species4
- Drosophila melanogaster is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. (wikipedia.org)
- The developmental period for D. melanogaster varies with temperature, as with many ectothermic species. (wikipedia.org)
- Criteria for inclusion: a paper must be the first description of the complete or near-complete genome of a species, and it must describe the DNA sequence as well as relevant sequencing methods and biological discoveries revealed by the initial sequencing of the genome. (fieldofscience.com)
- Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. (nyu.edu)
Novo1
- Chaisson, Wilson, Eichler (2015) emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. (speakerdeck.com)
Prediction1
- FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila. (flybase.org)
Consortium1
- Recently, the consortium has distributed a working draft assembly of the entire genome that removes redundancies, orients sequence fragments and clearly indicates gaps arising from sequencing and assembly. (biomedcentral.com)
Analyses1
- analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)
Flies2
- Drosophila melanogaster flies can sense air currents with the hairs on their backs. (wikipedia.org)
- The directed expression of Buffy in the dopamine producing neurons, via aDdc-Gal4 transgene, resulted in flies with increased climbing ability and enhanced survival, while the inhibition of Buffy in the dopaminergic neurons reduced climbing ability over time prematurely, similar to the phenotype observed in the alpha-synuclein-induced Drosophila model of PD. (sdbonline.org)
Chromosomal1
- Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. (bcm.edu)
Transcription3
- Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of Drosophila melanogaster. (bcm.edu)
- Regulation of Drosophila eye development by the transcription factor Sine oculis. (bcm.edu)
- The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. (oeaw.ac.at)
Assembly8
- The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. (inrae.fr)
- We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. (inrae.fr)
- We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. (biomedcentral.com)
- The assembly provides simplified descriptions of the genome, as disparate data sources such as GenBank and numerous expressed sequence tag (EST) and protein databases are unified. (biomedcentral.com)
- Single molecule assembly for genomes large and small. (speakerdeck.com)
- Automated ensemble assembly and validation of microbial genomes. (speakerdeck.com)
- Reducing assembly complexity of microbial genomes with single-molecule sequencing. (speakerdeck.com)
- Human genome assembly solved? (speakerdeck.com)
Model6
- The Top 10 Genome Papers include 5 bacteria, 3 model organisms, and the two human genome papers right at the top. (fieldofscience.com)
- Drosophila is a well-established model system, and the basic molecular mechanisms controlling its development are very similar to that of other animals, including humans. (ucla.edu)
- Harmonizing model organism data in the Alliance of Genome Resources. (flybase.org)
- Alliance of Genome Resources Portal: unified model organism research platform. (flybase.org)
- Subsequently, the expression of Buffy was altered in the alpha-synuclein-induced Drosophila model of PD. (sdbonline.org)
- It is concluded that the inhibition of Buffy in DA neurons produces a novel model of PD in Drosophila. (sdbonline.org)
Sequencing2
Clones1
- The sequence of these clones is approximately 93% complete to at least 4-fold coverage [ 7 ]. (biomedcentral.com)
Lineage1
- The paper "Expression-based cell lineage analysis in Drosophila through a course-based research experience for early undergraduates" is available online at G3 (doi: 10.1534/g3.119.400541). (ucla.edu)
Similarities1
- As the authors point out, the function of approximately 40-50% of the proteins encoded by each genome cannot be determined on the basis of similarities to proteins of known function. (biomedcentral.com)
Proteins2
- In the entire case of D. virilis and D. subobscura , it's been shown the fact that genomes of the types contain at least one duplicate of gypsy putatively encoding an entire envelope proteins [4]. (healthyguide.info)
- These results provide a mechanism by which Drosophila Bcl-2 family proteins can control apoptosis and shed light on a link between Rbf1 and mitochondrial dynamics, in vivo. (sdbonline.org)
Metabolic1
- Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. (nyu.edu)
Researchers1
- Relative to the fruit fly, the house fly genome contained far more repetitive sequence elements and copy number variants, the researchers noted, along with an especially robust representation of immune system components. (genomeweb.com)
Pest2
- D. melanogaster is a common pest in homes, restaurants, and other places where food is served. (wikipedia.org)
- NEW YORK (GenomeWeb) - A Cornell University-led team has sequenced and started analyzing the genome of the domestic house fly, Musca domestica , in the hopes of detecting genetic clues for dealing with the pest and pathogens it carries. (genomeweb.com)
Bacterial1
- This resulted in 105,697 contigs, which were annotated: most contigs had a best blastx hit to the pea aphid (phylogenetically closest complete genome), while very few bacterial hits were recorded (except for Probionibacterium acnes ). (biomedcentral.com)
Human3
- The Drosophila Genome Project was funded by the National Human Genome Research Institute , National Cancer Institute , and Howard Hughes Medical Institute . (bcm.edu)
- Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. (nyu.edu)
- Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease. (nyu.edu)
Data1
- And the data has been compiled into an online database (G-TRACE Expression Database) that serves as a resource for the Drosophila research community. (ucla.edu)
Analysis1
- Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster. (flybase.org)
Size2
- Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. (bcm.edu)
- The total assembled length is 3.08 billion bp - about 4% smaller than estimates of genome size based on flow cytometry [ 9 ], presumably due to the exclusion of constitutive heterochromatic regions and centromeres. (biomedcentral.com)
Evolutionary1
- These research were completed to comprehend the evolutionary behavior of gypsy and suggest that the hereditary firm of gypsy in those types is conserved. (healthyguide.info)
Features1
- Like the mammalian orthologues, Drosophila EYA features a N-terminal threonine and C-terminal tyrosine phosphatase domain. (cnrs.fr)
Study1
- To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. (natureasia.com)
Control2
- A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary. (oeaw.ac.at)
- The inhibition of porin under the control of neuronal Ddc-Gal4 result in short lifespan and in an age-dependent loss in locomotor function, phenotypes that are strongly associated with Drosophila models of Parkinson disease . (sdbonline.org)
Factors1
- The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila. (oeaw.ac.at)