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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
..., over 220 of which correspond to possible models for human diseases (Online Mendelian Inheritance in Animals [OMIA], Sydney School of Veterinary Science, https://omia.org/). Particularly, -wide association studies (GWASs) involving modest size cohorts of dogs have led to the identification of variants...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...and provide another layer of regulation to overall chromatin structure.In combination with post-translational modification of histones, eukaryotic s also establish diverse chromatin states using histone variants, encoded by stand-alone single-copy genes, which replace canonical histones in the nucleosome...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...variant and functional mechanism remain unclear. Increased sequencing coverage upstream of KIT has been detected in short-read sequenced Hereford and Simmental cattle, both of which have a characteristic white head (Whitacre 2014), suggesting that a copy number variant might contribute to this iconic...
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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
..., Dindot SV. 2012. Identification of copy number variants in horses. Genome Res 22: 899–907. ↵Duan J, Zhang JG, Deng HW, Wang YP. 2013. Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One 8: e59128. ↵Eden E, Navon R, Steinfeld I, Lipson D...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D during oncogenesis. In summary, our findings provide evidence for the loss of organization at multiple scales during breast cancer progression, revealing novel...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...MLST-based life identification number (LIN) codes can be used to classify KpSC s and to detect outbreak strains (Palma et al. 2024). Here, we aimed to investigate the accuracy of ONT assemblies from uncorrected SUP raw reads for these applications.K. pneumoniae species complexcgMLST profiles of ONT-assembled s...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
...version: In this window In a new window Figure 1. Identification of satellite-free centromeres in Equus asinus. ChIP-seq reads from primary fibroblasts of HorseS (A) and DonkeyA (B) were mapped on the EquCab2.0 horse reference . Immunoprecipitation was performed with an antibody against human CENPA (red...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
..., Veazy K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV. 2012. Identification of copy number variants in horses. Genome Res 22: 899–907. doi:10.1101/gr.128991.111 ↵Fulton JE, McCarron AM, Lund AR, Pinegar KN, Wolc A, Chazara O, Bed'Hom B, Berres M, Miller MM. 2016. A high-density SNP panel reveals...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...of silencing mechanisms that exist in plants and the importance of using disparate model species to discover these mechanisms.Transposable elements (TEs), or transposons, are mobile genetic elements that can change location and generate new copies in their host s. As a result, TEs populate eukaryotic s and can...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem...
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