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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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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
...to map genomic regions shaping quantitative traits with high spatial resolution 306 and statistical power sufficient to detect subtle effect sizes typical of natural genetic variation. 307 Incorporation of sequence data improves mapping resolution 308 We incorporated our WGS data to determine...
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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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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...-read technologies.In this Special Issue of Genome Research, we have assembled a diverse collection of articles highlighting novel methods, applications, and insights emerging from long-read technologies. This Special Issue contains four reviews, two perspectives, 16 research, and 17 method articles. While the long...
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Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
- Juri Kuronen,
- Samuel T. Horsfield,
- Anna K. Pöntinen,
- Sudaraka Mallawaarachchi,
- Sergio Arredondo-Alonso,
- Harry Thorpe,
- Rebecca A. Gladstone,
- Rob J.L. Willems,
- Stephen D. Bentley,
- Nicholas J. Croucher,
- Johan Pensar,
- John A. Lees,
- Gerry Tonkin-Hill,
- and Jukka Corander
Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
...approaches to -scale analysis of covariation at single-nucleotide resolution, termed as the -wide epistasis and coselection study (GWES), have demonstrated ample potential to uncover drivers of adaptation, virulence, survival, and antimicrobial resistance from densely sampled populations of major pathogens...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...regulation at multiple levels and revealing novel biological insights. We provide examples of using ggRibo to visualize different types of noncanonical ORFs in humans, Arabidopsis, rice, and tomatos. Additionally, we present examples that demonstrate how ggRibo can be applied to gain an in...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...scientific community.Genotype imputation servers (Das et al. 2016) are invaluable tools for the genomics community, providing streamlined analysis pipelines that enhance the quality and resolution of genotype data sets. By utilizing reference panels of high-quality s, these servers perform phasing...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...at Austin, Dell Pediatric Research Institute, Austin, Texas 78723, USA; 9Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; 10Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
.... freemani. The schematic (top left) illustrates the migration patterns of linear and circular DNA forms in 2D gel electrophoresis. The ethidium bromide stained gel (top right) with 2D-electrophoretically separated T. freemani genomic DNA was Southern-blotted and hybridized with TfSat01 (bottom left) and Tf...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...University, Ithaca, New York 14853, USA; 4Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA; 5Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA; 6Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000...

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