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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: 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
....marques@upf.eduAbstractExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive -wide...
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Research: Extensive variation in germline de novo mutations in Poecilia reticulata
- Yuying Lin,
- Iulia Darolti,
- Wouter van der Bijl,
- Jake Morris,
- and Judith E. Mank
Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
...individual sequencing read depth, and sites located in the repetitive genomic regions predicted as described above for filtering DNM sites. Lastly, SNPs that were heterozygous in either parent were excluded from the callable size estimation. The final callable size was intersected across each trio...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...cattle, characterized by complex pedigrees that are ideally suited to detect DNMs and by the systematic use of ART, to study the rate of de novo structural variation (dnSV) in this species and how it is impacted by IVF. By exploiting features of associated de novo point mutations (dnPMs) and dn...
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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
...crossovers to occur at specific locations in organisms that lack a functional copy of PRDM9. To get preliminary information about potential mechanistic underpinnings of recombination rate variation in wood whites, we assessed if specific sequence motifs or gene categories were enriched in recombination...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...Assembly of a pan for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...of different types of RNA for the four assemblies (Supplemental Table S6).Genomic characteristicsOf a total of 189,981 protein sequences in sheep, argali, and seven other species (i.e., human, dog, horse, pig, cattle, yak, and goat), we identified 19,917 gene families (orthogroups) based on homologous proteins...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...be ascertained. With the costs of sequencing dropping dramatically by using next-generation sequencing, emerging high-quality cattle genomic sequence will soon facilitate the application of this direct sequence comparison strategy. Approaches such as paired-end sequence mapping strategy have yielded massive...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
...regions and totaling ∼86.37 Mb of the horse . These data are consistent with estimates of copy number variation in humans and mice, suggesting that 5%–10% of the has undergone recent genomic rearrangements leading to copy number variation among individuals (Sharp et al. 2006; Stankiewicz and Lupski 2010...
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Method: SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk
- Wouter Coppieters,
- Latifa Karim,
- and Michel Georges
Genome Res. August 2020 30: 1201-1207; Published in Advance June 26, 2020, doi:10.1101/gr.256172.119
..., Browning SR. 2018. A one-penny imputed from next generation reference panels. Am J Hum Genet 103: 338–348. doi:10.1016/j.ajhg.2018.07.015 ↵Chan AW, Hamblin MT, Jannink J-L. 2016. Evaluating imputation algorithms for low depth genotyping-by-sequencing (GBS) data. PLoS One 11: e0160733. doi:10.1371/journal...

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