Searching journal content for articles similar to López-Cortegano et al. 33 (1): 45.

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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
.... The landscape of the ensuing rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii. In telomerase...
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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
...Biosciences (PacBio) long reads have been used to discover de novo mutations in MA lines of the green alga Chlamydomonas (López-Cortegano et al. 2023), revealing that 5% of mutations are SMs and highlighting the important contribution of active TEs in shaping the SM spectrum. Current estimates of SM rates...
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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
...characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across...
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Research: Accelerated rates of large-scale mutations in the presence of copper and nickel
- Frédéric J.J. Chain,
- Jullien M. Flynn,
- James K. Bull,
- and Melania E. Cristescu
Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
...of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103...
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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
...in mutation rate between the sexes or among wild individuals or populations.Apparent variation in mutation rate may also be partly attributable to a lack of precision in the estimates, as the challenge of accurately estimating the mutation rate can be formidable when one or fewer de novo mutations is expected...
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Research: High mutational rates of large-scale duplication and deletion in Daphnia pulex
- Nathan Keith,
- Abraham E. Tucker,
- Craig E. Jackson,
- Way Sung,
- José Ignacio Lucas Lledó,
- Daniel R. Schrider,
- Sarah Schaack,
- Jeffry L. Dudycha,
- Matthew Ackerman,
- Andrew J. Younge,
- Joseph R. Shaw,
- and Michael Lynch
Genome Res. January 2016 26: 60-69; Published in Advance October 30, 2015, doi:10.1101/gr.191338.115
...various classes of mutation (Tucker et al. 2013; So et al. 2015). In this study, we provide joint, -wide estimates of the rates and spectra of base-substitutionmutations, gene-conversionlike processes, and de novo copy-number variants (CNVs) for both cyclically parthenogenetic and obligately asexual D...
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Letter: Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila
- Geoffrey D. Findlay,
- Michael J. MacCoss,
- and Willie J. Swanson
Genome Res. May 2009 19: 886-896; doi:10.1101/gr.089391.108
...98195-5065, USA Abstract As genomic sequences become easier to acquire, shotgun proteomics will play an increasingly important role in genome annotation. With proteomics, researchers can confirm and revise existing genome annotations and discover completely new genes. Proteomic-based de novo...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
....1), and Chlamydomonas reinhardtii (release 5.5). The transcriptome of Ceratodon purpureus was de novo assembled using Trinity (Haas et al. 2013). To identify transcribed homologous sequences, TBLASTN (word size = 3) was performed using sORF peptide sequences as queries and the transcriptome sequences of the above...

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