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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
...and structurally variable regions in the , shaped by a complex dynamics of host-pathogen coevolution (for review, see Radwan et al. 2020). Beyond immunological significance, the MHC has thus become a prime model in evolutionary and comparative genomics, offering insights into birth-and-death processes, concerted...
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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
...NUMTs. It has been noted previously that some avian chromosomes have not been assembled in many bird s, such as Chromosome 16 (Laine et al. 2016), smaller microchromosomes (Kapusta et al. 2017), and the germline-restricted chromosome (Kinsella et al. 2019). This reduced ability to locate the precise genomic...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...High-quality assembly of the Chinese white truffle and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae Jacopo Martelossi1,2,8, Jacopo Vujovic3,8, Yue Huang3,4,8, Alessia Tatti2,5, Kaiwei Xu4, Federico Puliga3, Yuanxue Chen4, Omar Rota Stabelli2...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...Genetics and Genomics, Karolinska University Hospital, 17177 Stockholm, Sweden; 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 5Pacific Northwest Research Institute, Seattle, Washington 98122, USA Small supernumerary marker chromosomes (sSMCs) remain...
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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: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
.... 2023). Along these lines, it has been described recently that the degree of chromosome arm compaction during mitosis can differ across species (Kakui et al. 2022).Using genomics techniques, it was found that mitotic chromosomes can harbor cell type–specific features on a more detailed scale...
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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
...confidentiality and integrity of the computation. We introduce novel data-oblivious algorithmic techniques based on compressed reference panels and dynamic fixed-point arithmetic that comprehensively mitigate side-channel leakages in TEEs to provide robust protection of users’ genomic data throughout the analysis...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...regions (Christmas et al. 2023).Here, to identify reliable mammalian UCEs (mUCEs) and avian UCEs (aUCEs) using numerous species, we developed a comparative genomics approach that considers potential species-specific mutations and assembly errors without compromising length or quantity (Fig. 1). First, we...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...(e.g., Mohammed et al. 2022; Hansen et al. 2024) will also provide valuable insights into the role of gene regulation in shaping complex traits, from both biomedical and evolutionary perspectives.MethodsInput library generationWe generated input fragments by extracting genomic DNA from LCLs from 25...
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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
...on this comparison, we also draw conclusions about the genomic architecture, evolutionary dynamics, and the main molecular mechanisms that most significantly differentiated their satellitomes.ResultsIdentification of T. freemani satDNAsThe first step was to characterize the T. freemani satellitome. For assembly...

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