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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
...NUMT genes for mammals and birdsSelection analysis on NUMT gene clusters suggests positive and negative selection on NUMTsA proper evolutionary analysis of a single phylogenetically isolated NUMT gene is limited by the availability of the last mitochondrial lineage from which the mitochondrial DNA...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
....1086/418744 ↵Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK. 2004. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci 101: 3490–3494. doi:10.1073/pnas.0306582101 ↵Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila...
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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
...for DNA repair mechanisms in carnivores has been attributed to increased consumption of heme-related reactive oxygen species (Kim et al. 2016). Decreased heme-related disease risk may drive the observed pattern of relaxed evolutionary constraint as lineages become increasingly herbivorous...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...pathway. Across all treatments, between 68.4-96.6% of the transcripts and 111 between 33.3-92% of the proteins associated with the respective pathway were upregulated 112 (Figure 1C). 113 Selected members of the primary DNA repair pathways were further examined for each 114 treatment over time (Figure 1D...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...the GO analysis. (G) Differential transcript expression (log2 GSC/CySC) for select genes involved in DNA replication shows the higher expression of these genes in GSC-like cells (green bars). One gene, Cdc45, is differentially expressed in the CySC-like cells (magenta bar). (H) Confocal images of testis...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
.... 2H). These findings likely result from relaxed selection pressures in high-glucose cell culture conditions that may be permissive for accumulation of mtDNA variants that are deleterious in vivo. We note that this finding is of particular importance, given emerging technologies that culture patient...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...-specific feature optimization through its dual-adaptive mechanism. The selected optimal features are provided in Supplemental Table S7. From the perspective of species, the framework establishes a species-specific feature ranking R(s, k), which can capture the property differences of DNA sequences of different...
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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
...that play important biological functions. Gene Ontology (GO) analysis of UCE-adjacent genes further confirmed that conclusion. All UCEs were commonly enriched near genes that play multiple roles in the regulation of DNA transcription and RNA synthesis. Additionally, genes near UCEs were enriched for terms...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...are indicated in orange and dark blue, respectively. Additional selected metabolic pathways are indicated, including the mitochondrial ribosome (mito-ribosome), tricarboxylic acid cycle (TCA), and glycolysis. The lack of knowledge of regulators of mitonuclear gene expression is indicated.ResultsPostnatal mtDNA...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae. Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination...

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