SynthesisGenome biology2002
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Synthesis in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 201 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
201 citing papers in PubMed.
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- A transcriptome-wide systematic search does not detect A-to-I RNA editing inGenome research · 2026Article
- Defective transcription of AAGAG satellite DNA causes sex-ratio meiotic drive in Drosophila.Nature communications · 2026Article
- Defective transcription of AAGAG satellite DNA causes sex-ratio meiotic drive inbioRxiv : the preprint server for biology · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- A gene-based model of fitness and its implications for genetic variation: genetic and inbreeding loads.Genetics · 2025Article
- A gene-based model of fitness and its implications for genetic variation: linkage disequilibrium.Genetics · 2025Article
- Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.Molecular ecology · 2025Article
- A gene-based model of fitness and its implications for genetic variation: Linkage disequilibrium.bioRxiv : the preprint server for biology · 2025Article
- A gene-based model of fitness and its implications for genetic variation: Genetic and inbreeding loads.bioRxiv : the preprint server for biology · 2025Article
- A model of Hill-Robertson interference caused by purifying selection in a nonrecombining genome.Genetics · 2025Article
- Small ORFs, Big Insights:Cells · 2024Review
- Using FlyBase: A Database of Drosophila Genes and Genetics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Drosophila ribosome protein S5 paralog RpS5b promotes germ cell and follicle cell differentiation during oogenesis.Development (Cambridge, England) · 2021Article
- Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts.Nature communications · 2021Article
- Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models.BMC genomics · 2019Article
- Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution.Genes · 2019Article
- The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots.Molecular genetics and genomics : MGG · 2019Article
- Double triage to identify poorly annotated genes in maize: The missing link in community curation.PloS one · 2019Article
- Re-annotation of eightLife science alliance · 2018Article
141 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Funding
Abstract
backgroundThe recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
resultsAlthough the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
conclusionsIdentification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.