Searching journal content for articles similar to Uchimura et al. 25 (8): 1125.

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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
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...the different types of changes in the DNA sequence arise and their underlying mechanisms. New mutations are fundamental for many questions in evolutionary biology, and efforts to estimate their rates originated early in the history of genetics by phenotypic analysis of mutation accumulation (MA) lines...
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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
...will benefit future studies in population and evolutionary genetics.Mutation is the ultimate source of all genetic variation, and the mutation rate consequently plays a key role in evolutionary processes (Lynch 2010; Lynch et al. 2016). Although the germline mutation rate is thought to be lower than...
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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
...-performance genomics data visualization and exploration. Brief Bioinform 14: 178–192. Uchimura A, Higuchi M, Minakuchi Y, Ohno M, Toyoda A, Fujiyama A, Miura I, Wakana S, Nishino J, Yagi T. 2015. Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice...
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Method: Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
- Arikuni Uchimura,
- Hirotaka Matsumoto,
- Yasunari Satoh,
- Yohei Minakuchi,
- Sayaka Wakayama,
- Teruhiko Wakayama,
- Mayumi Higuchi,
- Masakazu Hashimoto,
- Ryutaro Fukumura,
- Atsushi Toyoda,
- Yoichi Gondo,
- and Takeshi Yagi
Genome Res. May 2022 32: 945-955; Published in Advance May 9, 2022, doi:10.1101/gr.276363.121
...mutations (Fig. 4A).The signature (Alexandrov et al. 2020) of mouse postzygotic mutations (validated mosaic mutations detected using deep-coverage WGS on five mice) resembled human postzygotic (Bizzotto et al. 2021) and mouse germline (de novo germline mutations accumulated in the long-term mouse inbreeding...
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Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...rates and patterns. Highlights of our results include: a high rate of multinucleotide mutation events at both short (∼5 bp) and long (∼1 kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and using our precise context-dependent mutation rates to predict long-term...
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Research: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
- Myrthe Jager,
- Francis Blokzijl,
- Ewart Kuijk,
- Johanna Bertl,
- Maria Vougioukalaki,
- Roel Janssen,
- Nicolle Besselink,
- Sander Boymans,
- Joep de Ligt,
- Jakob Skou Pedersen,
- Jan Hoeijmakers,
- Joris Pothof,
- Ruben van Boxtel,
- and Edwin Cuppen
Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
...for a single truncated Ercc1 allele, which largely corrupts protein function (Weeda et al. 1997; Dollé et al. 2011) and results in decreased NER-activity (Su et al. 2012). Ercc1−/Δ mice have five times shorter lives than wild-type (WT) littermates (Dollé et al. 2011; Vermeij et al. 2016). The livers of Ercc1...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...compared to primates (Li and Tanimura 1987; Li et al. 1996). In this hypothesis, most single nucleotide mutations occur during DNA replication in the male germline, and the larger number of passages associated with the rodent's shorter generation time accumulates more mutations in the same period of time...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
...families (Dewannieux et al. 2004; Ribet et al. 2004, 2008b). During our positional cloning efforts to identify the rat hd mutation (Krenova et al. 1999), we performed extensive sequencing of the critical region on chromosome 10 on the genomic and cDNA level (data not shown). Compared to wild-type reference...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...comprised 19,374 coding genes and as estimated by compleasm in protein mode, completely contains 99.91% of the mammalian BUSCO genes, which indicates a very high completeness.Long-term demographic history of the garden dormouseTo gain insight into the demographic history of the garden dormouse...

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