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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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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
..., collectively known as the Drosophila simulans species complex (or sim-complex) (Kliman et al. 2000), comprise the nearest sister species to D. melanogaster and are virtually equally related to each other (Fig. 1A), likely as a consequence of rapid speciation (Garrigan et al. 2012; Pease and Hahn 2013...
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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: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...at the transcriptional and the post-transcriptional level (Brennecke et al. 2007; Gunawardane et al. 2007; Sienski et al. 2012; Le Thomas et al. 2013). Most piRNAs are derived from discrete genomic source loci, termed piRNA clusters (Brennecke et al. 2007). In Drosophila melanogaster about 142 clusters were found, which...
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Research: A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
- Tina T. Hu,
- Michael B. Eisen,
- Kevin R. Thornton,
- and Peter Andolfatto
Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
...reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster , we also find...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...–664. doi:10.1101/gr.229202 ↵Khost DE, Eickbush DG, Larracuente AM. 2017. Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster. Genome Res 27: 709–721. doi:10.1101/gr.213512.116 ↵Kitchener AC, Breitenmoser-Würsten C, Eizirik E, Gentry A...
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Research: Impact of the X Chromosome and sex on regulatory variation
- Kimberly R. Kukurba,
- Princy Parsana,
- Brunilda Balliu,
- Kevin S. Smith,
- Zachary Zappala,
- David A. Knowles,
- Marie-Julie Favé,
- Joe R. Davis,
- Xin Li,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Jianxin Shi,
- Anshul Kundaje,
- Douglas F. Levinson,
- Philip Awadalla,
- Sara Mostafavi,
- Alexis Battle,
- and Stephen B. Montgomery
Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
...-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 18: 279–290. ↵Awadalla P, Boileau C, Payette Y, Idaghdour Y, Goulet JP, Knoppers B, Hamet P, Laberge C; CARTaGENE Project. 2013. Cohort profile of the CARTaGENE study: Quebec's population-based biobank...
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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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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
..., certain D. melanogaster/D. simulans hybrids lack the gene and are sterile. The finding of a gene involved in reproductive isolation in the ancestral Drosophila Y chromosome suggests a simple explanation for the key role of this chromosome in several cases of reproductive isolation between Drosophila...
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LETTER: Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome
- Emmanuelle Lerat,
- Carène Rizzon,
- and Christian Biémont
Genome Res. August 2003 13: 1889-1896; Published in Advance July 17, 2003, doi:10.1101/gr.827603
...cedex, France Abstract The availability of the sequenced Drosophila melanogaster genome provides an opportunity to study sequence variation between copies within transposable element families. In this study,we analyzed the 624 copies of 22 transposable element (TE) families (14 LTR...

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