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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...Heil et al. 2015). In insects, fine-scale maps of social and solitary bees have not revealed recombination hotspots (Wallberg et al. 2015; Jones et al. 2019), but there is evidence for hotspots in a butterfly (Torres et al. 2023).We find evidence that recombination is directed toward hotspots in both...
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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 the assumption that inversions catalyze recombination suppression between the X and Y Chromosomes, we found little evidence of XY structural variation. Using a high-density linkage map, we revealed that the large region of X–Y divergence was likely owing to the emergence of sex determining factors in the region...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...Yujie Chen1,2,3,7, Yiran Hou1,2,3,7,8, Qinglin Zeng1,2,3, Irene Wang1,2, Meiru Shang1,2, Kwangdeok Shin4, Christopher Hemauer1,2,9, Xiaoyun Xing1,2,3, Junsu Kang4, Guoyan Zhao1,5,6 and Ting Wang1,2,3 1Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA...
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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
...system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole- resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
.... maculatus compared with X. hellerii polymorphic elements revealed a global dispersion of TEs along chromosomes, some with accumulations at chromosome extremities, notably for X. maculatus (Supplemental Fig. S6).To assess impacts of the polymorphic TEs on genes, we identified those that localize close...
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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
...synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...million years represents a lower bound on the age of the X-Chromosome palindromes and that future high-resolution sequencing of mammalian X Chromosomes may reveal that these palindromes are conserved in more distantly related species.Primate X palindromes could be conserved because they are inherently...
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Method: De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
- Daniel Melamed,
- Yuval Nov,
- Assaf Malik,
- Michael B. Yakass,
- Evgeni Bolotin,
- Revital Shemer,
- Edem K. Hiadzi,
- Karl L. Skorecki,
- and Adi Livnat
Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
.... 2019).The results underscore the importance of mapping the mutation rate variation at an ultrahigh resolution. It is beyond this fact that several observations on the HbS mutation specifically can be mentioned. First, if one assumes that the HbS rate is the same for both of the continental groups...
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Research: Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system
- Dan Sun,
- Donna L. Maney,
- Thomas S. Layman,
- Paramita Chatterjee,
- and Soojin V. Yi
Genome Res. October 2019 29: 1673-1684; Published in Advance September 23, 2019, doi:10.1101/gr.248641.119
..., avian systems offer an excellent opportunity to investigate the evolution of sex chromosomes and the genomic impact of reduced recombination in general.We integrated recently generated nucleotide-resolution DNA methylation maps with comprehensive transcriptome data in the chicken. Similar to the s...

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