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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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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
..., Parsch J, Bornberg-Bauer E. 2023. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Res 33: 872–890. doi:10.1101/gr.277482.122 Hadjeras L, Heiniger B, Maaß S, Scheuer R, Gelhausen R, Azarderakhsh S, Barth-Weber S...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
..., with a mean identity of 93.6% (Fig. 2E).Fossil-calibrated and -scale divergence time reveals a late Cretaceous origin and Paleogene radiation of TuberaceaeTo provide a robust timeline for Tuberaceae emergence and diversification as well as a backbone for all comparative genomic analyses, we first produced...
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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
...sequence in Drosophila (Zile et al. 2020; Li et al. 2021). Recent studies using deep transcriptomics and ribosome-profiling identified thousands of species-specific sequences with evidence of transcription and translation that form the raw material for incipient de novo gene formation (Ruiz-Orera et al...
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Research: Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation
- Yi-Ru Li,
- Hsiao Wen Lai,
- Hsiao Han Huang,
- Hsing-Chun Chen,
- Sebastian D. Fugmann,
- and Shu Yuan Yang
Genome Res. June 2021 31: 1011-1023; Published in Advance April 15, 2021, doi:10.1101/gr.271148.120
...333 Taiwan; 3Department of Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan; 4Department of Gynecology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan Corresponding author: yangsy@mail.cgu.edu.twAbstractGerm cells in Drosophila melanogaster are specified...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...-induced misincorporation tRNA sequencing), an RNA-seq pipeline designed for tRNA analysis (Behrens et al. 2021), in our study of tsRNAs in Drosophila melanogaster. The library construction step of this pipeline includes necessary measures to minimize tRNA modifications that can hinder effective detection and quantitation...
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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
...-up analysis of gene–TE chimeras.MethodsFly stocksFive D. melanogaster strains obtained from the European Drosophila Population Genomics Consortium (DrosEU) were selected according to their different geographical origins: AKA-017 (Akaa, Finland), JUT-011 (Jutland, Denmark), MUN-016 (Munich, Germany), SLA-001...
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Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
- Chris Papadopoulos,
- Isabelle Callebaut,
- Jean-Christophe Gelly,
- Isabelle Hatin,
- Olivier Namy,
- Maxime Renard,
- Olivier Lespinet,
- and Anne Lopes
Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
...-defined and specific 3D structure as shown with the young de novo genes BSC4 and goddard identified in the S. cerevisiae and Drosophila melanogaster lineages, respectively (Namy et al. 2003; Bungard et al. 2017; Lange et al. 2021). In particular, Bungard et al. (2017) reported that the Bsc4 protein folds partially...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...illuminate their impact on dynamics and evolution (Gilbert et al. 2021). With more than 1 million described species, insects account for the bulk of Earth's animal biodiversity (Stork 2018). Although some insects have become model genetic organisms (e.g., Drosophila melanogaster) and thus considerable...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...)centromeric heterochromatin, recent studies revealed examples in which short arrays of (peri)centromeric satDNAs also spread to euchromatic regions. For example, (peri)centromeric satDNA families in humans, Drosophila, and the beetle Tribolium castaneum can also be dispersed within euchromatin in the form of clustered...
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