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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
...bioinformatic pipeline (Vendrami et al. 2022), we detected 85,100 NUMTs across 435 mammalian species (66.62%) and 28,947 NUMTs across 458 avian species (100%). These results align with earlier studies showing that NUMT integration is a frequent, ongoing process in vertebrates (Hazkani-Covo 2022). On average...
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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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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...Taurine pan uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle Sotiria Milia1,4, Alexander S. Leonard1,4, Xena Marie Mapel1, Sandra Milena Bernal Ulloa2, Cord Drögemüller3 and Hubert Pausch1 1Animal Genomics, ETH Zurich, Zurich 8092, Switzerland...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...persist until a polyadenylation signal or a new exon is encountered. For 5′ truncations, a promoter unlike that of the ancestral gene must be used if such duplicates are to be transcribed. Specific examples of known human-specific genes by type are indicated.Duplicated genomic segments of high sequence...
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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
...and that this organization is “neutral.”These are the most recent collations of host–nested genes in human from 2005 and 2008, respectively (Yu et al. 2005; Assis et al. 2008). Genomic annotation is now much more comprehensive and advances in measurement technologies detect transcript isoforms in a more systematic way...
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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
...Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 6McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA; 7Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA; 8Developmental Biochemistry, Biozentrum...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...is the implication of nonallelic homologous recombination (NAHR), usually responsible for TDDO (Zhang et al. 2013; Krasileva 2019). This mechanism can generate segmental duplications or deletions. In the 20rDNA L6F6, we detected duplications but no deletions, probably because of their deleterious effects.Two other...
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Research: The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
- Jeramiah J. Smith and
- Melissa C. Keinath
Genome Res. August 2015 25: 1081-1090; Published in Advance June 5, 2015, doi:10.1101/gr.184135.114
...-captured Petromyzon marinus. Integration of mapping data greatly improved the resolution of comparative maps, which provide strong support for a single ancient WGD but only weak support to a proposed second duplication. Comparative mapping data reveal the signatures of specific events (segmental duplications...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...(Marín-Béjar and Huarte 2015).The localization RIDLs discovered—MIR and LINE-2—are both ancient and contemporaneous, being active before the mammalian radiation (Cordaux and Batzer 2009). Both have previously been associated with acquired roles in the context of genomic DNA but not, to our knowledge...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...to the substantial cross-species size variation of conserved HMRs. Therefore, we find progressive extension a more likely hypothesis. Together, these observations suggest that recently appearing epigenomic features encompass smaller genomic intervals than more ancient features. Of note, such a global trend would...

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