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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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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
..., underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary assemblies. We generated highly contiguous de novo reference s for the Drosophila simulans species complex (D. simulans, D...
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Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
- Ying Zhen,
- Christian D. Huber,
- Robert W. Davies,
- and Kirk E. Lohmueller
Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
.... melanogaster, we used the Drosophila Population Genomics Project phase 3 data, including 197 African D. melanogaster lines from Zambia, Africa (Lack et al. 2015). For divergence, D. melanogaster and D. simulans genic alignments (Dmel v5/Dsim v2) were extracted from the multispecies alignments from Hu et al...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...(3R)C C 3R 92D1 100F2-3 16,000,000b 26,000,000b aNucleotide level breakpoints from Corbett-Detig and Hartl (2012). bApproximate physical breakpoints corresponding to cytological map. DGRP Freeze 2.0 Genome Research 1197 www..org tionarily with respect to Drosophila simulans and determined...
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Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
...using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades...
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Research: Direct estimate of the rate of germline mutation in a bird
- Linnéa Smeds,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. September 2016 26: 1211-1218; Published in Advance July 13, 2016, doi:10.1101/gr.204669.116
...in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 18: 279–290. Awadalla P, Gauthier J, Myers RA, Casals F, Hamdan FF, Griffing AR, CôtéM, Henrion E, Spiegelman D, Tarabeux J, et al. 2010. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet 87: 316...
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LETTER: No effect of recombination on the efficacy of natural selection in primates
- Kevin Bullaughey,
- Molly Przeworski,
- and Graham Coop
Genome Res. April 2008 18: 544-554; Published in Advance January 16, 2008, doi:10.1101/gr.071548.107
...studies that used divergence data ( Betancourt and Presgraves 2002 ) or divergence and polymorphism data ( Presgraves 2005 ) focused on genes in Drosophila melanogaster and Drosophila simulans , many of which were chosen because of prior evidence for positive selection. For these subsets of the Drosophila...
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