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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...large-scale sequencing efforts (Fig. 2D).Sequencing strategies will continue to update as new technologies become more accessible. Advances in long-read sequencing make it possible to capture the complexities of individual-level structure across human populations (Beyter et al. 2021). This technology...
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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain,1,2 Harmonie Barasc,3 Thomas Faraut,3 Anne Calgaro,3 Nathalie Bonnet,3 Camille Marcuzzo,4 Amandine Suin,4 Anne Barbat,2 Chris Hozé,1...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...and similarity, suggesting little large-scale genetic differentiation or degeneration of the Y Chromosome. Large-scale inversions are often thought to catalyze recombination suppression between the X and Y Chromosomes (Charlesworth et al. 2005), although there is little direct evidence of this, and other...
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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
...rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole- population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...or get fixed) (Maynard Smith and Haigh 1974; Cutter and Payseur 2013). Although -wide estimates of recombination rate and large-scale variation have been characterized for many species, detailed recombination maps are still mainly limited to model organisms and domesticated species, although little...
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Research: Individualized VDJ recombination predisposes the available Ig sequence space
- Andrei Slabodkin,
- Maria Chernigovskaya,
- Ivana Mikocziova,
- Rahmad Akbar,
- Lonneke Scheffer,
- Milena Pavlović,
- Habib Bashour,
- Igor Snapkov,
- Brij Bhushan Mehta,
- Cédric R. Weber,
- Jose Gutierrez-Marcos,
- Ludvig M. Sollid,
- Ingrid Hobæk Haff,
- Geir Kjetil Sandve,
- Philippe A. Robert,
- and Victor Greiff
Genome Res. December 2021 31: 2209-2224; Published in Advance November 23, 2021, doi:10.1101/gr.275373.121
...models. This suggests that, in addition to genetic, there is also nongenetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...3), mirroring previous large-scale observations using chicken WCP and BAC-FISH onto Apalone (O'Connor et al. 2018) and cDNA-FISH onto the Chinese softshell turtle Pelodiscus sinensis (Matsuda et al. 2005) (denoted Pelodiscus hereafter). This observation indicates that the fairly conserved karyotype...
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Research: The effect of recombination on the evolution of a population of Neisseria meningitidis
- Neil MacAlasdair,
- Maiju Pesonen,
- Ola Brynildsrud,
- Vegard Eldholm,
- Paul A. Kristiansen,
- Jukka Corander,
- Dominique A. Caugant,
- and Stephen D. Bentley
Genome Res. July 2021 31: 1258-1268; Published in Advance June 9, 2021, doi:10.1101/gr.264465.120
...), and this variation in recombination rate is particularly relevant amid the disruption of population structure caused by large-scale vaccine introduction (Potts et al. 2018).Burkina Faso, located in the center of the meningitis belt, historically has had a high burden of disease caused by serogroup A meningococci...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found...
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