Gene Model Annotations for<i>Drosophila melanogaster</i>: The Rule-Benders

Crosby, Madeline A.; Gramates, L. Sian; Santos, Gilberto dos; Matthews, Beverley; Pierre, Susan E. St.; Zhou, Pinglei; Schroeder, Andrew J.; Falls, Kathleen; Emmert, David B.; Russo, Susan M.; Gelbart, William M.

doi:10.1534/g3.115.018937

Cited by 23 publications

(27 citation statements)

References 84 publications

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“…Triple readthrough has been previously predicted for two D . melanogaster genes (Crosby et al 2015). …”

Section: Resultsmentioning

confidence: 99%

“…S9D, Supplementary Material online). Six of these 51 have been predicted to be readthrough transcripts previously (Crosby et al 2015). Combining these 51 with 282 reported in our 2011 paper gave us 333 D. melanogaster readthrough candidates to be used in our downstream analyses (fig.…”

Section: Resultsmentioning

confidence: 99%

“…The representation of readthrough genes in D . melanogaster by FlyBase as alternative transcripts with longer CDS regions (Crosby et al 2015) can serve as a model. Our techniques for finding readthrough genes should be applicable to any clade for which many genomes at the appropriate evolutionary distance have been sequenced and aligned, as is the case for bees (Kapheim et al 2015) and ants (Simola et al 2013).…”

Section: Discussionmentioning

confidence: 99%

“…Six of the 51 D . melanogaster candidates that we identified using homology have been previously reported (Crosby et al 2015), namely, FBtr0345369, FBtr0084814, FBtr0345432, FBtr0079306, FBtr0330312, and FBtr0330733.…”

Section: Methodsmentioning

confidence: 97%

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Evolutionary Dynamics of Abundant Stop Codon Readthrough

et al. 2016

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Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.

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“…Triple readthrough has been previously predicted for two D . melanogaster genes (Crosby et al 2015). …”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 97%

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Evolutionary Dynamics of Abundant Stop Codon Readthrough

et al. 2016

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“…The FlyBase BLAST tool allows sequence-based queries against annotated transcripts or proteins from the twelve Drosophila species mentioned above. For D. melanogaster , Sequence Ontology terms and controlled comments have been used extensively to describe gene models and transcripts (34,39). These enable queries for exceptional cases, such as all genes with dicistronic transcripts or all transcripts annotated with non-canonical translation start sites, using QueryBuilder or the ‘Simple’ tab of QuickSearch.…”

Section: Genomic Datamentioning

confidence: 99%

Using FlyBase, a Database of Drosophila Genes and Genomes

Marygold

Crosby

Goodman

2016

Methods in Molecular Biology

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SUMMARY For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic and high-throughput technologies add to the quantity and diversity of available data and resources. FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback. This chapter provides an overview of the data content, organization and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.

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