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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...-derived sequences (Lipatov et al. 2005). A recent transcriptome-wide study identified 327 genes in Drosophila melanogaster that generate chimeric transcripts across different populations (Oliveira et al. 2023). Among all genes, 76 generate chimeric transcripts from TE insertions that were present in one strain...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...identified in a West African and a European population of Drosophila melanogaster, and a European population of Drosophila simulans. (A) The genomic positions of the SNMs on chromosomes. Each gray bar represents the of one offspring. Point color represents mutation type and point shape represents...
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Research: Accelerated rates of large-scale mutations in the presence of copper and nickel
- Frédéric J.J. Chain,
- Jullien M. Flynn,
- James K. Bull,
- and Melania E. Cristescu
Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
...(Supplemental Table S1), similar to what has been found in earlier studies of Drosophila melanogaster and Caenorhabditis elegans (Lipinski et al. 2011; Schrider et al. 2013). Overall, partial gene CNVs exhibited the same general patterns as complete gene CNVs, with significantly higher rates in NiCu lines (Mann...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...-induced misincorporation tRNA sequencing), an RNA-seq pipeline designed for tRNA analysis (Behrens et al. 2021), in our study of tsRNAs in Drosophila melanogaster. The library construction step of this pipeline includes necessary measures to minimize tRNA modifications that can hinder effective detection and quantitation...
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Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
- Mariana Villalba de la Peña,
- Pauliina A.M. Summanen,
- Martta Liukkonen,
- and Ilkka Kronholm
Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
...than insertions when repeated sequences were excluded. Because deletions also tended to be longer, mutations have the tendency to reduce size. Similar patterns in mutational bias have been observed for Drosophila melanogaster (Leushkin et al. 2013). For repeated sequences, we analyzed homopolymer...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer and identification of drug resistance mutations Jonathan S. Brammeld,1 Mia Petljak,1 Inigo Martincorena,1 Steven P. Williams,1 Luz Garcia Alonso,2 Alba Dalmases,3 Beatriz Bellosillo,3 Carla Daniela Robles-Espinoza,4...
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Method: RNA-seq–based mapping and candidate identification of mutations from forward genetic screens
- Adam C. Miller,
- Nikolaus D. Obholzer,
- Arish N. Shah,
- Sean G. Megason,
- and Cecilia B. Moens
Genome Res. April 2013 23: 679-686; Published in Advance January 8, 2013, doi:10.1101/gr.147322.112
.... Identification of EMS-induced mutations in Drosophila melanogaster by whole- sequencing. Genetics 182: 25–32. Bowen ME, Henke K, Siegfried KR, Warman ML, Harris MP. 2012. Efficient mapping and cloning of mutations in zebrafish by low coverage whole sequencing. Genetics 190: 1017–1024. Brenner S. 1974...
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Method: Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster
- Bing He,
- Amy Caudy,
- Lance Parsons,
- Adam Rosebrock,
- Attilio Pane,
- Sandeep Raj,
- and Eric Wieschaus
Genome Res. December 2012 22: 2507-2519; Published in Advance June 28, 2012, doi:10.1101/gr.137406.112
...Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster Bing He 1 , Amy Caudy 2 , Lance Parsons 2 , Adam Rosebrock 3 , Attilio Pane 1 , Sandeep Raj 1...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
..., and turn to the study of the Trichoplax or Loxodonta s. There remains much to discover, and many resources are now available to catalyze discovery by individual research groups ( Matthews et al. 2005 ), who will remain the bedrock of the Drosophila community in the post-genomic era ( Gilbert 1991 ). Large-scale...
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RESOURCE: Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster
- Roger A. Hoskins,
- Alexander C. Phan,
- Mohammed Naeemuddin,
- Felipa A. Mapa,
- David A. Ruddy,
- Jessica J. Ryan,
- Lynn M. Young,
- Trent Wells,
- Casey Kopczynski,
- and Michael C. Ellis
Genome Res. June 1, 2001 11: 1100-1113; Published in Advance May 14, 2001, doi:10.1101/gr.178001
...in Drosophila melanogaster rely on a chromosome carrying multiple dominant or recessive marker mutations with visible phenotypes. These visible phenotypes are often laborious to score and may interfere with the phenotype of the mutant of interest. Most importantly, because mutations with easily scored, viable...

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