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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
...the green and red arrow paths, respectively, indicate the sequence preceding and following the segmental duplication. (B) Repeat structure within the candidate SV region, for five classes of genomic elements. The start and end sequences are taken from A, whereas the full copy refers to the 14.3 kb segmental...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...genes by virtue of multiple paralogous sequence variants. We examined 19 gene families as expressed in developing and adult human brain, selected for their high sequence identity (average >99%) and overlap with human-specific segmental duplications (SDs). We characterized the transcriptional differences...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...), compared with quantitative blotting-based estimates of 35 (Burg et al. 1989). Copy number at this locus was stable, in that for all of the queried II×III F1 progeny, the copy number for each was identical to the parent from which it obtained that chromosomal segment. In contrast to the B1 locus, the “529...
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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
...drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding in dogs.The domestic dog has increasingly been...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
...and pan graphs improved sequence read mapping and removed biases in variant discovery (Crysnanto and Pausch 2020). Despite these improvements, the unique genetic diversity and SVs of Chinese indicine cattle are not reflected in any high-quality genomic resources currently available, despite the fact...
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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: 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
...by population-scale sequencing. Nature 470: 59–65. ↵ Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. 2009. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res 19: 491...
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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
...). SAMtools v1.10 (Li et al. 2009) was used to select reads with paired information. Duplicates were eliminated with MarkDuplicatesSpark as implemented in GATK v4.1.4.1 (McKenna et al. 2010) with the ‐‐remove-sequencing-duplicates option.Variant calling and filteringGATK's v4.1.4.1 HaplotypeCaller (McKenna et...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...: independently acquired multicopy and ampliconic genes (presumably from autosomal progenitor genes) with testis-specific expression. Ampliconic genes are distinguished from multicopy genes in that they reside in segmentally duplicated sequences that share >99% identity. If ampliconic gene content accounts for...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
..., and large segmental duplications with high sequence similarity between duplications (Bork and Copley 2001; Eichler 2001). Such efforts reveal a massive amount of genetic information that has been impenetrably cloaked by previous sequencing efforts and hence unable to be included in many biological...

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