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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...). One key insight from comparative studies is that the well-characterized genomic organization seen in mice and humans (the long-standing gold standard for MHC genomic research) is actually a derived state, specific to placental mammals. In humans, the MHC spans 4–5 Mb and contains well over 200 genes...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...that these arrays are embedded in conserved genomic regions, with >90% similarity in the 10-kb flanking regions (Supplemental Fig. S15). However, the PCA showed species-specific clustering of repeats (Fig. 6A), suggesting that the ∼40-kb array was present in the common ancestor but diverged through gene conversion...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...(Supplemental Fig. S4), supporting the idea that the Y Chromosome of classical inbred strains originated from Japanese house mice (Japanese fancy mouse) (Bishop et al. 1985; Nagamine et al. 1992; Tucker et al. 1992; Takada et al. 2013).View larger version: In this window In a new window Figure 2. Geographic...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
..., Farmington, CT 060329 ∗ equal contribution † corresponding authors10 Running title: Epigenetic variation in nine inbred mouse strains11 Abstract12 The diversity outbred (DO) mice and their inbred founders are widely used models of human disease.13 However, although the genetic diversity of these mice has...
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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
...in inbred mouse s (Garretson et al. 2025).The biological mechanisms underlying the elevated rate of dnSNVs in ART-derived mice remain unclear. Known mutational processes often leave distinct genomic signatures, including signatures attributable to oncogenic processes (Alexandrov et al. 2020) and germline...
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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
...found to be common but tend to be present in populations at low frequencies, owing to their deleterious effects (Chakraborty et al. 2019). This suggests that they contribute to a genomic architecture of rare alleles with high effect sizes and could reveal new insights concerning the genomic architecture...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16: e1008926. doi:10.1371/journal.pgen.1008926 ↵Campbell P, Good JM, Nachman MW. 2013. Meiotic sex chromosome inactivation is disrupted in sterile hybrid male house mice. Genetics 193: 819...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...contribute to genomic diversification driven by the acquisition of adaptive elements across species.An intriguing possibility for the acquisition of novel, genetically adapted elements is the transfer of organelle DNA (Popadin et al. 2022; Butenko et al. 2024). In many eukaryotic species, organelles...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...These authors contributed equally to this work. Corresponding author: matthew.webster@imbim.uu.seAbstractMeiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...poses a significant challenge in maintaining practical performance under privacy constraints. Here, we introduce TX-Phase, a secure haplotype phasing method based on the framework of trusted execution environments (TEEs). TX-Phase allows users’ private genomic data to be phased while ensuring data...
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