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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
...a role, we scanned the s of more than 1000 avian and mammalian species for NUMTs. We show that a subclass of divergent NUMTs harboring mitogenes with intact reading frames is widespread across mammals and birds. We also show that some of these NUMTs appear to be similar across species. In addition, we...
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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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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
...origin followed by bacterial origin (Fig. 8A). When we further separate the G4 clusters by eukaryotic taxonomic subdivisions, we find that non-mammalian vertebrates and plants have the largest number of G4 clusters (Fig. 8B). The distribution of sequences based on their detection method shows...
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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
...for evidence of complete PRDM9 genes (Fig. 4A), which could potentially govern the presence of recombination hotspots in these s, as it has been shown to do in mammalian s (Baudat et al. 2010; Myers et al. 2010; Parvanov et al. 2010). The C. secundus contains a PRDM9 homolog (XP_023708049.2) with annotated...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...window Figure 1. Species selection for comparative genomic analyses of mammalian diet. The carnivory score represents the proportion of the diet composed of animal-based food items for each species, as listed in EltonTraits (Wilman et al. 2014). This score was used as input in our RERconverge analyses...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...of miR-7 by the Oip5os1 (also known as Cyrano) long noncoding RNA (lncRNA) in mammalian tissues (Kleaveland et al. 2018).Questions also remain regarding the rates of miRNA turnover and the extent to which degradation is regulated in a miRNA-specific manner. Most miRNAs that have been examined are highly...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...of similarity scores was computed and converted into genomic coverage according to the coverage of the TE family. The right extremity of the graph corresponds to recent (highly similar) TE insertions.To evaluate the impact of TEs on divergence, we searched for polymorphic insertions between pairs of species...
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Research: A quantitative framework for characterizing the evolutionary history of mammalian gene expression
- Jenny Chen,
- Ross Swofford,
- Jeremy Johnson,
- Beryl B. Cummings,
- Noga Rogel,
- Kerstin Lindblad-Toh,
- Wilfried Haerty,
- Federica di Palma,
- and Aviv Regev
Genome Res. January 2019 29: 53-63; Published in Advance December 14, 2018, doi:10.1101/gr.237636.118
...- and species-specific phenotypes.Multiple studies have analyzed expression data collected across mammalian species using various heuristic methods for defining conserved and divergent expression levels (Chan et al. 2009; Brawand et al. 2011; Merkin et al. 2012; Perry et al. 2012). However, there is currently...
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Method: Iterative epigenomic analyses in the same single cell
- Hidetaka Ohnuki,
- David J. Venzon,
- Alexei Lobanov,
- and Giovanna Tosato
Genome Res. October 2021 31: 1819-1830; Published in Advance February 24, 2021, doi:10.1101/gr.269068.120
...in digital/binary-like, sparse sequencing reads. Furthermore, existing single-cell epigenomic technologies cleave genomic DNA and discard the single cells after single use, preventing reanalysis of the same single cell to confirm the results and collect data of additional epigenetic marks. To account...

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