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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on mutational processes shaping two functionally important tandem arrays in the Drosophila .ResultsGenome assembliesThe strains selected include the Drosophila community's reference strain (iso-1) (Adams et al. 2000) and two strains from the Drosophila Synthetic Population Resource (A3 and A4) (King et al. 2012...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...).The fungal data set includes 74 fungal s which were selected according to the method of Wang et al. (2009) as representative of the fungal diversity, together with three outgroup s: Caenorhabditis elegans, Drosophila melanogaster, and Monosiga brevicollis. All proteomes and s were downloaded from...
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Method: Increased taxon sampling reveals thousands of hidden orthologs in flatworms
- José M. Martín-Durán,
- Joseph F. Ryan,
- Bruno C. Vellutini,
- Kevin Pang,
- and Andreas Hejnol
Genome Res. July 2017 27: 1263-1272; Published in Advance April 11, 2017, doi:10.1101/gr.216226.116
...lengths decrease BLAST sensitivity (Moyers and Zhang 2015). We thus expected hidden orthologs to consist of significantly shorter proteins, as is seen in Drosophila orphan genes (Palmieri et al. 2014). When analyzed together, the length of the flatworm hidden ortholog transcripts is not significantly...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...sequence in Drosophila (Zile et al. 2020; Li et al. 2021). Recent studies using deep transcriptomics and ribosome-profiling identified thousands of species-specific sequences with evidence of transcription and translation that form the raw material for incipient de novo gene formation (Ruiz-Orera et al...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...means that the neORF is found only in one line. The y-axis represents the neORFs length. The four boxes on the right represent the average lengths of de novo genes found in Drosophila with different ages. (B) Number of exons in neORFs. The x-axis shows the genomic position of neORFs. The y-axis shows...
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Research: Mendelian randomization analyses implicate biogenesis of translation machinery in human aging
- Sara Javidnia,
- Stephen Cranwell,
- Stefanie H. Mueller,
- Colin Selman,
- Jennifer M.A. Tullet,
- Karoline Kuchenbaecker,
- and Nazif Alic
Genome Res. February 2022 32: 258-265; Published in Advance January 25, 2022, doi:10.1101/gr.275636.121
...effects on organismal growth in Drosophila (Lin et al. 2011; Marshall et al. 2012). Additionally, a recent report indicates that improved fidelity of translation can also promote longevity in the fruit fly (Martinez-Miguel et al. 2021).Ethical considerations and costs of clinical trials severely limit...
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Research: Less effective selection leads to larger genomes
- Tristan Lefébure,
- Claire Morvan,
- Florian Malard,
- Clémentine François,
- Lara Konecny-Dupré,
- Laurent Guéguen,
- Michèle Weiss-Gayet,
- Andaine Seguin-Orlando,
- Luca Ermini,
- Clio Der Sarkissian,
- N. Pierre Charrier,
- David Eme,
- Florian Mermillod-Blondin,
- Laurent Duret,
- Cristina Vieira,
- Ludovic Orlando,
- and Christophe Jean Douady
Genome Res. June 2017 27: 1016-1028; Published in Advance April 19, 2017, doi:10.1101/gr.212589.116
..., it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/ by-nc/4.0/. Research 1016 Genome Research 27:1016–1028 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org www..org testing of the MH...
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Method: OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
..., Caenorhabditis elegans, Drosophila melanogaster, Acyrthosiphon pisum, Capitella sp., Helobdella robusta, and Lottia gigantea were downloaded from the OMA database website. The combined set of 30 nonredundant protein sets contained 19 lophotrochozoans, four deuterostomes, four ecdysozoans, and proteomes from...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
..., as is a paralog of Cdk9, Lsk1 (Fig. 8B). In S. cerevisiae, the orthologous cyclin-dependent Pol II kinase complex Ctk1/Ctk2/Ctk3 (Lsk1/Lsc1 in S. pombe) was recently shown to bind RNA in the nanomolar range (Battaglia et al. 2017). To assess RNA binding of S. pombe Cdk9 in vitro, we coexpressed full-length S...
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Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
- Eskeatnaf Mulugeta,
- Evelyne Wassenaar,
- Esther Sleddens-Linkels,
- Wilfred F.J. van IJcken,
- Edith Heard,
- J. Anton Grootegoed,
- Walter Just,
- Joost Gribnau,
- and Willy M. Baarends
Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
...across mammals. Nature 508: 488–493. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, et al. 2011. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet 43...

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