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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
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...significance (GUS) that are difficult to interpret, even with the integration of the latest bioinformatic tools. In this Perspective, we review how studies using the fruit fly Drosophila melanogaster have facilitated rare disease diagnosis by uncovering the clinical relevance of GUS and classifying rare...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites...
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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
...of de novo genes that emerged within a single species. We sequenced and assembled s with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few ne...
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Research: Death of new microRNA genes in Drosophila via gradual loss of fitness advantages
- Guang-An Lu,
- Yixin Zhao,
- Hao Yang,
- Ao Lan,
- Suhua Shi,
- Zhongqi Liufu,
- Yumei Huang,
- Tian Tang,
- Jin Xu,
- Xu Shen,
- and Chung-I Wu
Genome Res. September 2018 28: 1309-1318; Published in Advance July 26, 2018, doi:10.1101/gr.233809.117
...constraints. Noncoding genes, especially small ones, are freer to evolve de novo by comparison. The best examples are microRNAs (miRNAs), a large class of regulatory molecules ∼22 nt in length. Here, we study six de novo miRNAs in Drosophila, which, like most new genes, are testis-specific. We ask how and why...
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Research: Evidence for the fixation of gene duplications by positive selection in Drosophila
- Margarida Cardoso-Moreira,
- J. Roman Arguello,
- Srikanth Gottipati,
- L.G. Harshman,
- Jennifer K. Grenier,
- and Andrew G. Clark
Genome Res. June 2016 26: 787-798; Published in Advance April 12, 2016, doi:10.1101/gr.199323.115
...duplicates are initially fixed within populations and later maintained in s. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...“orphans”), including rapid divergence from functional genes, inadequacies of search strategies, and de novo birth from noncoding sequences without a genic precursor (Khalturin et al. 2009; Tautz and Domazet-Lošo 2011; Van Oss and Carvunis 2019).The mystery surrounding the origin of ORFans is fundamental...
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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
...data, up to one-third of genes in a given organism are classified as orphan genes that do not have recognizable homologs in other phylogenetic lineages (Toll-Riera et al. 2009; Tautz and Domazet-Lošo 2011). Although the formation of new genes from previously noncoding sequences was initially thought...
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LETTER: Reverse Transcriptase-Polymerase Chain Reaction Validation of 25 “Orphan” Genes from Escherichia coli K-12 MG1655
- Jean-Philippe Alimi,
- Olivier Poirot,
- Fabrice Lopez,
- and Jean-Michel Claverie
Genome Res. July 1, 2000 10: 959-966; doi:10.1101/gr.10.7.959
...Reverse Transcriptase-Polymerase Chain Reaction Validation of 25 “Orphan” Genes from Escherichia coli K-12 MG1655 Jean-Philippe Alimi , Olivier Poirot , Fabrice Lopez , and Jean-Michel Claverie 1 Structural and Genetic Information...
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12 Drosophila Genomes/Letter: Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
- Andreas Heger and
- Chris P. Ponting
Genome Res. December 2007 17: 1837-1849; Published in Advance November 7, 2007, doi:10.1101/gr.6249707
...Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Andreas Heger 1 and Chris P. Ponting MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom...
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