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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
...to facilitate rapid adaptive radiation to new hosts. To test this hypothesis, we selected six Drosophila species/subspecies from the repleta group with different primary cacti hosts.No positive selection in columnar cacti dwellers versus Opuntia sp. dwellersThe necrotic tissue of each cactus-host used...
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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: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene–TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference s available. We found that ∼19% of body part...
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Research: Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations
- Shuo Zhang,
- Beverly Pointer,
- and Erin S. Kelleher
Genome Res. April 2020 30: 566-575; Published in Advance April 1, 2020, doi:10.1101/gr.251546.119
...nuclear and cytoplasmic actors of the piRNA pathway and induces cis-spreading of piRNA production. Genetics 201: 1381–1396. doi:10.1534/genetics.115.180307 ↵Hill T, Schlötterer C, Betancourt AJ. 2016. Hybrid dysgenesis in Drosophila simulans associated with a rapid invasion of the P-element. PLoS Genet 12...
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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: Cellular abundance shapes function in piRNA-guided genome defense
- Pavol Genzor,
- Parthena Konstantinidou,
- Daniel Stoyko,
- Amirhossein Manzourolajdad,
- Celine Marlin Andrews,
- Alexandra R. Elchert,
- Constantinos Stathopoulos,
- and Astrid D. Haase
Genome Res. November 2021 31: 2058-2068; Published in Advance October 19, 2021, doi:10.1101/gr.275478.121
...et al. 2020).In Drosophila, a genomic region of more than 100 kilobases (kb), flamenco (lncRNA:flam), has long been known as a major transposon control region (Supplemental Fig. S1B; Lin and Spradling 1997; Sarot et al. 2004; Wu et al. 2020). This essential piRNA cluster looks like a transposon...
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Research: piRNA-mediated transgenerational inheritance of an acquired trait
- Thomas Grentzinger,
- Claudia Armenise,
- Christine Brun,
- Bruno Mugat,
- Vincent Serrano,
- Alain Pelisson,
- and Séverine Chambeyron
Genome Res. October 2012 22: 1877-1888; Published in Advance May 3, 2012, doi:10.1101/gr.136614.111
...-element, we report here that in such Drosophila ovaries, the initiation of a ping-pong cycle is exclusively achieved by secondary I-element piRNAs that are produced in the ovary and deposited in the embryonic germline. This unusual secondary piRNA biogenesis, detected in the absence of functional I...
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Research: Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
- Yuliya A. Sytnikova,
- Reazur Rahman,
- Gung-wei Chirn,
- Josef P. Clark,
- and Nelson C. Lau
Genome Res. December 2014 24: 1977-1990; Published in Advance September 29, 2014, doi:10.1101/gr.178129.114
...noncoding RNAs (lncRNAs) driven by their unique TE landscapes and the Piwi pathway. Results TheDrosophilaOSS cell line expresses only primary piRNAs and the single PIWI protein since it is derived from the follicle cells of the Drosophila ovary (Niki et al. 2006; Lau et al. 2009; Haase et al. 2010). As such...
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Letter: Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
- Jian Lu and
- Andrew G. Clark
Genome Res. February 2010 20: 212-227; Published in Advance November 30, 2009, doi:10.1101/gr.095406.109
...to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster , our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more...
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Resource: Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
- Bryan B. Teefy,
- Ari Adler,
- Alan Xu,
- Katelyn Hsu,
- Param Priya Singh,
- and Bérénice A. Benayoun
Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
...trajectories in addition to just gonadal aging end points. Indeed, we found that many key events, including those relating to TE regulation and piRNA pathway regulation, are most salient in middle-aged ovaries, rather than undergoing linear changes with age. Our observations differ from reports in Drosophila...

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