title: Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.
abstract: We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15-18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138 bmatthew@morgan.harvard.edu.
authors.forename: Beverley B
authors.initials: BB
authors.lastname: Matthews
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Dos Santos
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Madeline A
authors.initials: MA
authors.lastname: Crosby
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: David B
authors.initials: DB
authors.lastname: Emmert
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Susan E
authors.initials: SE
authors.lastname: St Pierre
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: L Sian
authors.initials: LS
authors.lastname: Gramates
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Pinglei
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schroeder
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Falls
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Victor
authors.initials: V
authors.lastname: Strelets
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Russo
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.
authors.forename: William M
authors.initials: WM
authors.lastname: Gelbart
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics*; D005091:Exons; D005260:Female; D008297:Male; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D058727:RNA, Small Untranslated
keywords: alternative splice; exon junction; lncRNA; transcription start site; transcriptome