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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
...Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear s Yu-Chi Chen1,2, David L.J. Vendrami3,4,5,6, Maximilian L. Huber2, Luisa E.Y. Handel2, Christopher R. Cooney7, Joseph I. Hoffman3,4,5,6,8 and Toni I. Gossmann1,2,3,5 1Computational Systems Biology, Faculty...
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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
...nucleosome remodeling and is accompanied by local transcription changes and chromatin reorganization, and subsequently may contribute to the stabilization of broken chromosomes. Our findings highlight the resilience and adaptability of plant chromosomes in response to centromere breakage and provide valuable...
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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
...in these tissues experience a relaxation of evolutionary constraint in more herbivorous lineages.As a diversity of mammalian diets arose from the ancestral insectivorous strategy (Gill et al. 2014), numerous physiological, morphological, and behavioral adaptations also evolved. Understanding the mechanisms...
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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
...Africa Corresponding authors: diana.lobo@cibio.up.pt, rgodinho@cibio.up.ptAbstractUnderstanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...a strong role in suppressing transposon mobilization and genomic dysregulation. I reasoned that with ∼40% of a typical mammalian consisting of repetitive elements, skimming can assess methylation at the transposon family level by averaging methylation across all copies of a family.To determine the minimum...
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Research: The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
- Li Ren,
- Wuhui Li,
- Qinbo Qin,
- He Dai,
- Fengming Han,
- Jun Xiao,
- Xin Gao,
- Jialin Cui,
- Chang Wu,
- Xiaojing Yan,
- Guoliang Wang,
- Guiming Liu,
- Jia Liu,
- Jiaming Li,
- Zhong Wan,
- Conghui Yang,
- Chun Zhang,
- Min Tao,
- Jing Wang,
- Kaikun Luo,
- Shi Wang,
- Fangzhou Hu,
- Rurong Zhao,
- Xuming Li,
- Min Liu,
- Hongkun Zheng,
- Rong Zhou,
- Yuqin Shu,
- Yude Wang,
- Qinfeng Liu,
- Chenchen Tang,
- Wei Duan,
- and Shaojun Liu
Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
...and various cis and trans regulations were observed from F1 to F3 in the two hybrid lineages. These asymmetric patterns of gene expression represent the alternative strategies for counteracting deleterious effects of the subs and improving adaptability of novel hybrids. Furthermore, we identified positive...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...for this deviation from the prediction of the theory may lie in the adaptability offered by a higher mutation rate, as we were able to show that the of the widely studied Hydra magnipapillata strain 105 has undergone a process of strong positive selection since the strain's cultivation 50 years ago. This most likely...
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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
...rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced s with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird s, respectively. Our results show...
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Method: Targeted, programmable, and precise tandem duplication in the mammalian genome
- Yaoge Jiao,
- Min Li,
- Xingyu He,
- Yanhong Wang,
- Junwei Song,
- Yun Hu,
- Li Li,
- Lifang Zhou,
- Lurong Jiang,
- Junyan Qu,
- Lifang Xie,
- Qiang Chen,
- and Shaohua Yao
Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122
...Targeted, programmable, and precise tandem duplication in the mammalian Yaoge Jiao1,4, Min Li1,4, Xingyu He1,4, Yanhong Wang1,4, Junwei Song1, Yun Hu1, Li Li1, Lifang Zhou1, Lurong Jiang1, Junyan Qu2, Lifang Xie3, Qiang Chen1 and Shaohua Yao1 1Department of Biotherapy, Cancer Center and State Key...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...of the mammalian . This highlights the relevance of transcriptional crosstalk between genes which share nucleic acid sequence. The results and analysis are available on an Rshiny application (https://hngeneviewer.sites.er.kcl.ac.uk/hn_viewer/).Classically genes are represented one after another along...
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