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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
...hybridization (FISH) analysis, the probes guanine nucleotide-binding protein alpha-q (GNAQ; green signal) on the short arm and serine threonine kinase 39 (STK39; red signal) on the long arm of Chromosome 2 were mapped onto two acrocentric chromosomes of argali (Fig. 1C). We further examined the chromosomal...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...-C chromosome conformation capture data for both phasing and scaffolding of the assembly graph and supports both short-read Hi-C as well as Nanopore-based Pore-C (Deshpande et al. 2022) sequencing data. Critically, Verkko integrates this long-range linkage information directly with the assembly graph, improving...
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RESOURCE: An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci
- Jillian F. Maddox,
- Kizanne P. Davies,
- Allan M. Crawford,
- Dennis J. Hulme,
- Daniel Vaiman,
- Edmond P. Cribiu,
- Bradley A. Freking,
- Ken J. Beh,
- Noelle E. Cockett,
- Nina Kang,
- Christopher D. Riffkin,
- Roger Drinkwater,
- Stephen S. Moore,
- Ken G. Dodds,
- Joanne M. Lumsden,
- Tracey C. van Stijn,
- Sin H. Phua,
- David L. Adelson,
- Heather R. Burkin,
- Judith E. Broom,
- Johannes Buitkamp,
- Lisa Cambridge,
- William T. Cushwa,
- Emily Gerard,
- Susan M. Galloway,
- Blair Harrison,
- Rachel J. Hawken,
- Stefan Hiendleder,
- Hannah M. Henry,
- Juan F. Medrano,
- Korena A. Paterson,
- Laurent Schibler,
- Roger T. Stone,
- and Beryl van Hest
Genome Res. July 1, 2001 11: 1275-1289; Published in Advance June 12, 2001, doi:10.1101/gr.135001
..., 18, 20, 22, 23, 24, and X) regions of many chromosomes. As compared with the second generation ovine linkage map ( de Gortari et al. 1998 ), the number of marker intervals &gt;20 cM and 10 cM in the best positions map has reduced from 40 and 126 to 6 and 88, respectively. There are 11 gaps of &gt;20...
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LETTER: A Genetic Linkage Map of the Apicomplexan Protozoan Parasite Eimeria tenella
- Martin W. Shirley and
- Dora A. Harvey
Genome Res. October 1, 2000 10: 1587-1593; doi:10.1101/gr.149200
...development or resistance to an anticoccidial drug. The markers were placed in 16 linkage groups (which defined 12 chromosomes) and a further 57 unlinked groups. Two linkage groups showed an association ( P = .0105) with the traits of precocious development or drug-resistance and were mapped to chromosome 2...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep...
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ARTICLE: A second-generation linkage map of the bovine genome.
- S M Kappes,
- J W Keele,
- R T Stone,
- R A McGraw,
- T S Sonstegard,
- T P Smith,
- N L Lopez-Corrales,
- and C W Beattie
Genome Res. March 1997 7: 235-249; doi:10.1101/gr.7.3.235
....-M. White, R.L. Buetow, K.H. and Nishimura. D.Y. 1991 . The CEPH consortium linkage map of human chromosome 1. Genomics 9 : 686 – 700 . Ede, A.J., , Peirson, C.A. , Henry, H. , Crawford. A.M. Ede, A.J., Peirson, C.A. Henry, H. and Crawford. A.M. 1994 . Ovine microsatellites at the OarAE64, OarHH22, OarHH56...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within...
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LETTER: Human–Ovine Comparative Sequencing of a 250-kb Imprinted Domain Encompassing the Callipyge (clpg) Locus and Identification of Six Imprinted Transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8
- Carole Charlier,
- Karin Segers,
- Danny Wagenaar,
- Latifa Karim,
- Stéphane Berghmans,
- Olivier Jaillon,
- Tracy Shay,
- Jean Weissenbach,
- Noelle Cockett,
- Gabor Gyapay,
- and Michel Georges
Genome Res. May 1, 2001 11: 850-862; doi:10.1101/gr.172701
...on distal OAR18q ( Fahrenkrug et al. 2000 ; Shay et al. 2001 ), constructed an ovine BAC contig spanning that interval ( Segers et al. 2001 ), and refined the map position of the clpg locus by breakpoint analysis to a ≤400 kb chromosome segment flanked by microsatellite markers MULGE5 and OY3 ( Berghmans et...
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RESEARCH: Comparative Gene Mapping: A Fine-Scale Survey of Chromosome Rearrangements between Ruminants and Humans
- Laurent Schibler,
- Daniel Vaiman,
- Anne Oustry,
- Corinne Giraud-Delville,
- and Edmond P. Cribiu
Genome Res. September 1, 1998 8: 901-915; doi:10.1101/gr.8.9.901
...isolated from gene-containing bacterial artificial chromosomes (BACs), were added to the previous goat genetic map, achieving 88% genome coverage. Finally, 124 microsatellites were cytogenetically mapped, which made it possible to physically anchor and orient all the linkage groups. We believe...

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