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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
...Figs. S1, S2).Combining trio-based genomic and Hi-C data from F1 hybrids enabled construction of chromosome-span haplotypes that included 99.33% of all heterozygous single-nucleotide variants (SNVs; about 4.54 per kb) for each F1 hybrid (see Methods) (Supplemental Fig. S3). Through SNV phasing combined...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...Splice exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 BRCA1 and 72 BRCA2 variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...short-read sequencing (Logsdon et al. 2020; Cohen et al. 2022; Conlin et al. 2022). For example, long-read sequencing has improved interrogation of clinically significant regions, including structural variants, repeat expansions, homologous gene families, and the HLA region, as well as the inherent...
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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
.... thaliana, although synapsis and segregation of homologous chromosomes remain defective (Da Ines et al. 2012; Lao et al. 2013).View larger version: In this window In a new window Figure 1. Methodology of mapping recombination intermediates using Dmc1 knockout hybrid founders. (A) Key steps in mammalian...
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Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan,
- Andy Lin,
- Richard T. Wang,
- Joshua S. Bloom,
- Kenneth Lange,
- and Desmond J. Smith
Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
...@mednet.ucla.eduAbstractGenetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...-specific ID: (PTR) Pan troglodytes, (GGO) Gorilla gorilla, (PPA) Pan paniscus, (MMU) Macaca mulatta, (PAB) Pongo abelii, (PPY) Pongo pygmaeus. Numbers 1 and 2 represent parental homolog IDs of given sample assembly.Discontinuous alignments and large structural variantsOne of the advantages of the new...
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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
...new regulatory elements in support of the Britten–Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...GS library. As ExpansionHunter is intended to run on PCR-free srGS data, it was not run on this sample (Dolzhenko et al. 2019). This variant is reported as pathogenic in the literature (Amiel et al. 2003), is a strong match to the proband's observed symptoms, and was confirmed independently by additional...
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Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
...such as scRNA-seq and scATAC-seq have become widespread and effective tools to interrogate tissue composition. Increasingly, variant callers are being applied to these methodologies to resolve the genetic heterogeneity of a sample, especially in the case of detecting the clonal architecture of a tumor...

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