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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...Taurine pan uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle Sotiria Milia1,4, Alexander S. Leonard1,4, Xena Marie Mapel1, Sandra Milena Bernal Ulloa2, Cord Drögemüller3 and Hubert Pausch1 1Animal Genomics, ETH Zurich, Zurich 8092, Switzerland...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...; and neofunctionalization, in which duplicates evolve new functions (Taylor and Raes 2004; Hahn 2009; Kondrashov 2012; Kuzmin et al. 2022). Genome sequencing has supported the view that whole- duplication (WGD) events frequently occur during evolution across all domains of life, with many plant species retaining polyploid...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...located within the duplicated region. (F) Copy numbers of CSMD1 and MICU3 after passaging proband cells for 12, 22, 33, 40, and 50 passages. Mean ± SEM; data from representative trials are shown (n ≥ 3 total trials). Genomic DNA from the near-diploid MCF10A cell line was used as a control...
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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
..., presumably via accelerated recombination during fbxn gene duplication, thereby reinforcing genetic divergence among populations and between species.An unusually conserved genomic region is identified surrounding Cni-neib-1Given the highly dynamic nature of fbxn genes across C. nigoni populations...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
....pantalacci@ens-lyon.fr, marie.semon@ens-lyon.frAbstractSpecies adapting to a similar lifestyle may undergo convergent changes in organ structure and cellular function, themselves relying or not on these convergent genetic changes. The extent of genomic convergence is thus debated and may further depend on the interplay between...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...adaptive immunity, and MHC genes serve as key models in evolutionary genomics, offering insight into birth-and-death evolution, gene duplication, and the maintenance of genetic diversity. However, the organization and evolution of the MHC in species with giant s, such as salamanders, remain poorly...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...Tax. Different colors indicate different strains. The gray and colored rectangles in the pan graphs indicate the shared and unique genomic segments among strains, respectively. Arrows with the same color spell the path of a strain. The bold paths and dashed paths in the pan graphs indicate the existent...
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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
...of these regions in chimpanzees and gorillas. Detailed analyses of the composition of the associated terminal 32 bp satellite array from chimpanzee (termed pCht) and intervening segmental duplication (SD) spacers confirm two independent origins in the Pan and gorilla lineages. In chimpanzee and bonobo, we estimate...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...(GE Healthcare).Hi-CHi-C Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics) according to the manufacturer's instructions. For each cell line (10A, T1, C1) 1 million cells were used per Hi-C reaction. Cells were fixed with 1.2% formaldehyde for 12 min...

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