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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
.... The first relates to comparative genomics of MGEs across the Asgard archaea and beyond, including investigations across diverse environments and temporal studies. Using enrichments of Asgard archaea or, if they become available, pure cultures, experimental studies could test the adaptive significance...
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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
...and coding sequences (CDSs) (Fig. 3B). However, this analysis did not examine the G4 positioning relative to functional genomic sites. Based on G4Hunter methodology, we also find that in eukaryota, the median 24.2% of total genes per species harbor one or more G4s, whereas in archaea 10.1% of total genes...
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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
...contribute to genomic diversification driven by the acquisition of adaptive elements across species.An intriguing possibility for the acquisition of novel, genetically adapted elements is the transfer of organelle DNA (Popadin et al. 2022; Butenko et al. 2024). In many eukaryotic species, organelles...
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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: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...-quality reads and adapters were removed using fastp (v0.20.1) (Chen et al. 2018). The cleaned reads were aligned to the near gap-free reference of CS (Liu et al. 2025; Wang et al. 2025) using BWA-MEM (v0.7.17) with default parameters (Li and Durbin 2009). Genomic data visualization was facilitated using...
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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
...of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...These authors contributed equally to this work. Corresponding author: matthew.webster@imbim.uu.seAbstractMeiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates...
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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
.... 2025. Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA. Genome Res (this issue) 35: 644–652. doi:10.1101/gr.279240.124 ↵Horsfield ST, Fok BCT, Fu Y, Turner P, Lees JA, Croucher NJ. 2025. Optimizing nanopore adaptive sampling for pneumococcal serotype...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...to human-dominated landscapes.To test the “introgression fueled adaptation” hypothesis, we conducted a comprehensive genomic analysis of 48 historical (1912–2005) and 97 contemporary samples of Iberian wolves, alongside 67 worldwide wolves and 131 dogs (Fig. 1A,B; Supplemental Table S1). We used these data...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...-free regions, suggesting that much HT-induced mutational damage occurs during cell-cycle phases when genomic DNA is packaged into nucleosomes. We conclude that stressful experimental temperature increases accelerate plant mutation rates and particularly accelerate the rate of indel mutation. Increasing...

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