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  • Review Article
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Research resources for Drosophila: the expanding universe

Key Points

  • Drosophila melanogaster is one of the most powerful research models in modern biology.

  • Extensive public Drosophila research resources are vital to making Drosophila a valuable experimental system.

  • Resources for the Drosophila genus will significantly expand with the addition of whole-genome sequences for 11 other Drosophila species.

  • Research tools for D. melanogaster are comprehensive and include a high-quality, well-annotated whole-genome sequence, extensive collections of characterized mutations and a wealth of genetic and molecular reagents for manipulating the genome.

  • Public databases that are available online comprise key research resources and cover a wide range of information.

  • FlyBase is the principal repository and access point for Drosophila information.

  • Public collections of genetic stocks and molecular reagents provide universal access to an extensive range of sophisticated research materials.

  • Research services provide broad access to both routine techniques and specialized experimental protocols.

Abstract

Drosophila melanogaster has been the subject of research into central questions about biological mechanisms for almost a century. The experimental tools and resources that are available or under development for D. melanogaster and its related species, particularly those for genomic analysis, are truly outstanding. Here we review three types of resource that have been developed for D. melanogaster research: databases and other sources of information, biological materials and experimental services. These resources are there to be exploited and we hope that this guide will encourage new uses for D. melanogaster information, materials and services, both by those new to flies and by experienced D. melanogaster researchers.

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Acknowledgements

This work was supported by grants from the US National Science Foundation's Living Stock Collections Program and the following US National Institutes of Health bodies: National Human Genome Research Institute (NHGRI), National Center for Research Resources (NCRR), National Institute of General Medical Sciences (NIGMS) and National Institute of Child Health and Human Development (NICHHD).

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Correspondence to Kathleen A. Matthews.

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Glossary

WHOLE-GENOME SHOTGUN SEQUENCING

A method of sequencing large genomes in which an effectively random sampling of sequencing reads is collected from a target genome. The sequence of the original intact DNA is inferred on the basis of overlap among the fragments.

FINISHED SEQUENCE

Complete sequence of a clone or genome, with a defined level of accuracy and contiguity.

POLYTENE CHROMOSOME

A giant chromosome that is formed by many rounds of replication of the DNA. The replicated DNA molecules tightly align side-by-side in parallel register, which creates a non-mitotic interphase chromosome that is visible by light microscopy.

BALANCER CHROMOSOMES

Structurally rearranged chromosomes that prevent meiotic recombination between homologues. Because typical balancers are recessive lethal or sterile and carry visible mutations, they are used to create and maintain stable heterozygous stocks of lethal and sterile mutants.

DEFICIENCY

(Also known as a deletion.) A chromosome aberration in which the DNA encoding a portion of two or more genes is missing from the chromosome. Single gene or intragenic deletions are treated as alleles in the Drosophila melanogaster nomenclature.

PARALOGUE

One of a set of homologous genes in the same species that have evolved from a gene duplication and can be associated with a subsequent divergence of function.

BLAST

(Basic Local Alignment Search Tool.) A sequence comparison algorithm, optimized for speed, that is used to search sequence databases for optimal local alignments to a query.

CONTIG

Overlapping series of clones or sequence reads (for a clone contig or sequence contig, respectively) that correspond to a contiguous segment of the source genome.

ORTHOLOGY

Describes genes in different species that derive from a common ancestor.

SYNTENY

The state of genes being located on the same chromosome. In current usage, this typically refers to the order of genes within a chromosomal segment. Syntenic relationships among genes can be conserved over large evolutionary distances.

GENE ONTOLOGY

Three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner.

TRANSCRIPTOME ARRAYS

Microarrays that are designed to include probes to the entire mRNA complement that is expressed by an organism.

SEGMENTATION GENE

One of a group of genes that specify the segmental pattern within the anterior–posterior body axis of Drosophila and other arthropods.

SCAFFOLDS

(Also known as supercontigs.) Genomic units that are composed of one or more contigs that have been ordered and orientated using end-read information.

CG SYMBOL

A unique symbol composed of an integer prefixed with CG that is assigned to each D. melanogaster gene identified through annotation of the whole genome shotgun sequence. A CG symbol is the valid gene symbol in the absence of gene symbols that are based on mutant phenotype, molecular feature or determined function.

UPSTREAM ACTIVATING SEQUENCE

A yeast regulatory region that binds the transcriptional activator GAL4 and, when bound, activates the expression of an associated gene. Used in Drosophila in conjunction with GAL4 to control the induction of gene expression.

GAL4 DRIVER LINE

A line that expresses the yeast transcriptional activator GAL4 under the control of an inducible or a tissue-specific promoter. When crossed to an effector line that carries the upstream activator sequence (UAS) fused to a gene of interest, progeny with both the GAL4 and UAS components express the gene of interest in an activator-specific manner.

FLP RECOMBINASE TARGET

(FRT). Components of a recombination system that is adapted from the Saccharomyces cerevisiae 2μ plasmid. FLP encodes a site-specific recombinase, and FRT is the target site for the Flp recombinase. Expression of FLP mediates excision of any sequence that is flanked by FRT sites.

MOSAIC ANALYSIS WITH A REPRESSIBLE CELL MARKER

A system for mosaic analysis that allows the visualization of mutant cells but not heterozygous parent cells or homozygous wild-type siblings.

MOSAIC ANALYSIS

The process of creating and assessing the fate of clonally derived groups of cells that are genetically distinct from cells of the surrounding tissues.

ENHANCER-TRAP INSERTIONS

Genomic insertions of a transgenic construct used to identify genes that are expressed in specific tissues. When the construct inserts near a tissue-specific enhancer, the weak promoter on the construct comes under the control of the enhancer, resulting in tissue-specific expression of the reporter gene.

TAXONOMIC KEY

A device that is used to identify unfamiliar organisms and is usually based on a series of paired statements that describe contrasting morphological characteristics. Also known as a dichotomous key.

IMAGINAL DISCS

In holometabolous insect larvae, these are tissues that give rise to the external adult structures, such as the wing, eye and antennae.

HAEMOCYTES

Blood cells of invertebrates.

MONOCLONAL ANTIBODIES

Purified antibodies that are derived from single clones that recognize single antigens.

HYBRIDOMA

A hybrid cell line that is created by fusing a mortal antibody-producing B-lymphocyte with an immortalized myeloma line. The hybridoma line is immortal and produces a continuous supply of a particular monoclonal antibody.

FOSMID

A low-copy-number cosmid vector that is based on the Escherichia coli F-factor replicon. Cloned sequences are more stable in fosmids than in multi-copy vectors.

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Matthews, K., Kaufman, T. & Gelbart, W. Research resources for Drosophila: the expanding universe. Nat Rev Genet 6, 179–193 (2005). https://doi.org/10.1038/nrg1554

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