Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

By S. Misra, Madeline A. Crosby, C. Mungall, B. Matthews, K. S. Campbell, Pavel Hradecky, Yanmei Huang, J. Kaminker, G. Millburn, Simon Prochnik and 20 more. Genome Biology, 2002

376 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ef41d10cc136073b22a28e34099dcfee5d5b0a31

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Citations in the corpus

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies (2007, positive): “The Drosophila genome annotation is highly supported by experimental evidence (MISRA et al. 2002), hence the frequency of these discrepancies was surprising, but a”
FlyBase: genes and gene models (2004, methodology): “0 at the time of writing (5–7), has been enhanced by hand curation of all gene models (8,9), including integration of error reports submitted by the user community.”
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005, background): “By contrast, recent advances in the ﬁeld of gene annotation indicate that high-quality gene models can be produced by combining multiple independent sources of computational evidence [4–9].”
The relationship between non-protein-coding DNA and eukaryotic complexity. (2007, background): “which comprises only 1,000 cells, has 50% more annotated protein-coding genes ( 19,300 genes)((54)) than the far more complex insects ( 13,500 genes)((55)) and nearly as many”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “Some of these unexpected patterns might indicate that a gene is still missing in the analyzed set of protein sequences from one or more of the species included; reports of newly discovered genes have appeared since the release of the initial reports on genome sequences of complex eukaryotes, for exa”
A beginner's guide to eukaryotic genome annotation (2012, background): “Although this results in high-quality annotation 76,77 , it is so labour-intensive that, for budgetary reasons, smaller genome projects are increasingly being forced to rely on automated annotations.”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, methodology): “To predict new structures, we applied EvoFold 7 in highly conserved segments of the 12 Drosophila species and focused on high-stringency candidates with strong support by compensatory changes (Supplementary Methods 4).”
The Sequence Ontology: a tool for the unification of genome annotations (2005, background): “Several groups including SGD and FlyBase now use either SO or SOFA terms in their annotation efforts.”
Protein interaction mapping: a Drosophila case study. (2005, methodology): “1 (Adams et al. 2000; Celniker et al. 2002; Misra et al. 2002) and/or GenBank databases using a dedicated integrated laboratory production management system, the PIMBuilder (Rain et al. 2001).”
Diversity and dynamics of the Drosophila transcriptome (2014, positive): “Drosophila antisense transcription has been reported 34 , but the catalog of antisense transcription has been largely limited to mRNA-mRNA overlaps.”
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, positive): “Early large-scale genome projects relied heavily on the manual annotation of gene structures in order to ensure genome annotation of the highest quality [28-30].”