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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
..., Bergero R. 2021b. PromethION sequencing and assembly of the of Micropoecilia picta, a fish with a highly degenerated Y chromosome. Genome Biol Evol 13: evab171. doi:10.1093/gbe/evab171 ↵Cimino MC. 1974. The nuclear DNA content of diploid and triploid Poeciliopsis and other poeciliid fishes with reference...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...from 47,115 nuclear SNP loci. (A) Group assignment via five PCs obtained by a discriminant analysis of principal components. The predicted assignment of genetic clusters (K) 1–3 is shown by four different colors and the a priori sampling region identity is highlighted by dotted gray lines and text...
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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
...al. 2020; Karlsson et al. 2022), immunological (Dawson et al. 2013), and genetic (Groenen et al. 2012; Warr et al. 2020; Zhao et al. 2021) similarities with humans. The ability to generate -editing mutations in the pig combined with somatic nuclear cloning procedures has resulted in a number of new...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...approach suitable to infer selection for nuclear integrated mitochondrial sequences.View larger version: In this window In a new window Figure 5. Schematic illustration of the single gene and clustered genes codeml analysis. (A) Foreground branch in red (dN/dS = ω1) for a single NUMT gene; background...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...were developed for three-generation families and, in the case of Halldorsson et al. (2019), rely on long-range phasing information from a large cohort with known genealogy, which make them difficult to apply to family-based data sets that include only nuclear families.Building off of previous work...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...Assembly of a pan for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D...
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Method: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
- Yi Wang,
- James Lu,
- Jin Yu,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112
...An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data Yi Wang 1 , 2 , 5 , James Lu 1 , 3 , 5 , 6 , Jin Yu 1 , Richard A. Gibbs 1 , 4 and Fuli Yu 1 , 4 , 6 1...
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LETTER: Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats
- Carlos A. Driscoll,
- Marilyn Menotti-Raymond,
- George Nelson,
- David Goldstein,
- and Stephen J. O'Brien
Genome Res. March 1, 2002 12: 414-423; doi:10.1101/gr.185702
...window Table 1. Percent Polymorphic Loci and Percent Average Heterozygosity for Different Nuclear Gene Families in Free-Living Populations of Cheetahs, Lions, and Pumas RESULTS AND DISCUSSION Population History in Three Felidae Species Previously, African cheetahs sampled from eastern, southwestern...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
.... (2019) suggested that the subterminal heterochromatin was driving ectopic recombination by helping to form bouquet structures among nonhomologous chromosomes during late meiotic prophase, somewhat akin to the nuclear organizing structures associated with the repeat-rich short arms of mammalian...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...bp intervals with perfect identity and no genes annotated (Table 3; Fig. 3B; Supplemental Figs. S2, S3; Supplemental Table S3). Whereas the first interval is characterized by a high GC content (66%), the second one corresponds to a long interspersed nuclear element (LINE) (Table 3; Supplemental Figs...

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