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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...and Asian aboriginal Tibetan pigs. Using the F1 hybrid progeny, we then examine how allelic differences in 3D chromatin architecture broadly affect gene expression, and eventually phenotype, at multiple levels.ResultsConstruction of high-resolution diploid Hi-C contact mapsTo generate chromosome...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...Kohei Hagiwara, Andrew Thrasher, Nadezhda V. Terekhanova, and Jinghui Zhang Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA Allele-specific expression (ASE) of somatic mutations can be caused by cis-activation of the mutant allele...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
.... The standard approach is to generate a mutation on one parental background, and then the mutant allele is moved to the other background by sequential backcrossing. The original and the backcrossed strain are then bred together to generate an F1 knockout. Generating a sufficiently clean F1 hybrid is essential...
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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
...the possibility of combining alleles that diverged within different species lineages in an inter-species hybrid. Therefore, creating F1 interspecies hybrids provides a perfect tool for identifying phenotypes that are under control of incompatible genetic interactions (i.e., negative epistasis). Further...
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Method: Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
- Arikuni Uchimura,
- Hirotaka Matsumoto,
- Yasunari Satoh,
- Yohei Minakuchi,
- Sayaka Wakayama,
- Teruhiko Wakayama,
- Mayumi Higuchi,
- Masakazu Hashimoto,
- Ryutaro Fukumura,
- Atsushi Toyoda,
- Yoichi Gondo,
- and Takeshi Yagi
Genome Res. May 2022 32: 945-955; Published in Advance May 9, 2022, doi:10.1101/gr.276363.121
...to reconstruct cell lineages. We identified mosaic mutations in mice using deep whole- sequencing and reconstructed embryonic cell lineages based on the variant allele frequencies of the mutations. The reconstructed trees were confirmed using nuclear transfer experiments and the genotyping of approximately 50...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...hybridizations have been documented in Saccharomyces species. For instance, the wild S. paradoxus SpC* lineage present in North America (Eberlein et al. 2019) and the domesticated S. cerevisiae Alpechin lineage (D'Angiolo et al. 2020) are classic examples of past hybridizations that played genomic and phenotypic...
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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
....bartscherer@uni-osnabrueck.deAbstractIn contrast to other mammals, the spiny mouse (Acomys) regenerates skin and ear tissue, which includes hair follicles, glands, and cartilage, in a scar-free manner. Ear punch regeneration is asymmetric with only the proximal wound side participating in regeneration. Here, we show that cues originating from...
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Method: Generation of mouse conditional knockout alleles in one step using the i-GONAD method
- Renjie Shang,
- Haifeng Zhang,
- and Pengpeng Bi
Genome Res. January 2021 31: 121-130; Published in Advance December 16, 2020, doi:10.1101/gr.265439.120
...alleles require improvement. Here, we aim to develop and test a new approach by integrating a unique design of asymmetric loxP-ssODNA with the i-GONAD delivery method to create mouse conditional alleles.ResultsExploiting the i-GONAD method to create a conditional allele: a proof-of-principle test...
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Research: Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
...by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X...

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