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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: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...identified in a West African and a European population of Drosophila melanogaster, and a European population of Drosophila simulans. (A) The genomic positions of the SNMs on chromosomes. Each gray bar represents the of one offspring. Point color represents mutation type and point shape represents...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...dysregulation observed in ART-derived embryos could secondarily alter the genomic distribution and rate of new mutations compared with naturally conceived embryos (Mani et al. 2019). Second, the first few embryonic cell divisions are especially error-prone and uniquely vulnerable to the accumulation of large...
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Research: Temperature dependence of spontaneous mutation rates
- Ann-Marie Waldvogel and
- Markus Pfenninger
Genome Res. September 2021 31: 1582-1589; Published in Advance July 23, 2021, doi:10.1101/gr.275168.120
...for the non-biting midge Chironomus riparius (Diptera). G3 (Bethesda) 10: 1151–1157. doi:10.1534/g3.119.400710 ↵Schrider DR, Houle D, Lynch M, Hahn MW. 2013. Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster. Genetics 194: 937–954. doi:10.1534/genetics.113...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...of SNVs, indels, and additional structural variants. Our data show a rapid accumulation of mutations over a short evolutionary time span during the adult life of D. melanogaster.DiscussionWe have applied whole- sequencing to interrogate how spontaneous tumors arise from stem cells in the Drosophila...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...into exons or introns of protein-coding genes; a fourth instance may be termination of mRNAs from adjacent genes. The possibility remains that TRs are specifically transcribed into ncRNAs (Subirana and Messeguer 2021), as is known to occur for some loci in the Drosophila melanogaster (Biswas et al. 2024...
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Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
- Mariana Villalba de la Peña,
- Pauliina A.M. Summanen,
- Martta Liukkonen,
- and Ilkka Kronholm
Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
...than insertions when repeated sequences were excluded. Because deletions also tended to be longer, mutations have the tendency to reduce size. Similar patterns in mutational bias have been observed for Drosophila melanogaster (Leushkin et al. 2013). For repeated sequences, we analyzed homopolymer...
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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
...and Drosophila melanogaster s (Britten and Kohne 1968; International Human Genome Sequencing Consortium 2001; Treangen and Salzberg 2012; Hoskins et al. 2015). These sequences include repeated tandem arrays of noncoding sequences like satellite DNAs, self-replicating selfish elements like transposable elements...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...of mutation rate upon temperature was first identified in Drosophila melanogaster (Muller 1928). However, with the exception of detailed studies in Escherichia coli (Chu et al. 2018) and yeast (Huang et al. 2018), systematic whole- sequencing (WGS) investigations of the effects of temperature on mutation rate...
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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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