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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
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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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: 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
...Evolution of structure in the Drosophila simulans species complex Mahul Chakraborty1,7, Ching-Ho Chang2,7,8, Danielle E. Khost2,3, Jeffrey Vedanayagam4, Jeffrey R. Adrion5, Yi Liao1, Kristi L. Montooth6, Colin D. Meiklejohn6, Amanda M. Larracuente2 and J.J. Emerson1 1Department of Ecology...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...fly Drosophila melanogaster (Gerstein et al. 2010; Brown et al. 2014). Splice isoforms are often differentially expressed across tissues and/or during development (for select examples, see Pan et al. 2008; Wang et al. 2008; Gerstein et al. 2010; Ramani et al. 2011; Brown et al. 2014). As such...
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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
...eukaryotic transposons, into naive lines of Drosophila erecta. We monitored the invasion in three replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs, and the transcriptome at regular intervals. A piRNA-based host defense was rapidly established...
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Research: Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity
- Xinhai Ye,
- Chun He,
- Yi Yang,
- Yu H. Sun,
- Shijiao Xiong,
- Kevin C. Chan,
- Yuxuan Si,
- Shan Xiao,
- Xianxin Zhao,
- Haiwei Lin,
- Yang Mei,
- Yufeng Yao,
- Gongyin Ye,
- Fei Wu,
- and Qi Fang
Genome Res. September 2023 33: 1554-1567; Published in Advance October 5, 2023, doi:10.1101/gr.277707.123
...innovations (Arbuckle 2020; Zancolli and Casewell 2020). Moreover, venom presents excellent opportunities for investigating the emergence of new gene functions and the evolution of novel regulatory networks. Different venomous animals have developed diverse venom genes for distinct purposes (Casewell et al...
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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: 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: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
- Lili Tang,
- Fei Huang,
- Wuxin You,
- Ansgar Poetsch,
- Rafael Henrique Nóbrega,
- Deborah Mary Power,
- Tengfei Zhu,
- Kaiqiang Liu,
- Hong-Yan Wang,
- Qian Wang,
- Xiwen Xu,
- Bo Feng,
- Manfred Schartl,
- and Changwei Shao
Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
...temperatures could cause temperature-sensitive protein Prp8 inactivation to reduce the amounts of U4/U6.U5 triple small nuclear ribonucleoprotein particle (snRNP) complexes (Brown and Beggs 1992; Kuhn et al. 1999; Grainger and Beggs 2005). In Drosophila, such a process increases by 10-fold the output of circ...
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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
...reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.MicroRNAs (miRNAs) are an extensive class of ∼22-nt RNAs that play important regulatory roles in diverse eukaryotic species (Flynt and Lai 2008; Axtell et al. 2011). In the canonical metazoan pathway...

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