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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...Haplotype-resolved and population genomics of the threatened garden dormouse in Europe Paige A. Byerly1,2,16, Alina von Thaden1,2,16, Evgeny Leushkin1,3, Leon Hilgers1,3, Shenglin Liu1,3, Sven Winter4,5, Tilman Schell1,3, Charlotte Gerheim1,3, Alexander Ben Hamadou1,3, Carola Greve1,3, Christian...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
.... taeniatus Moliwe population is highly inbred (Langen et al. 2011), and laboratory experiments revealed active kin-mating preferences in this species, indicating that inbreeding is tolerated and even might be beneficial under certain conditions (Thünken et al. 2007). To compare the performance of offspring...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...Haplotype and population structure inference using neural networks in whole- sequencing data Jonas Meisner and Anders Albrechtsen Department of Biology, Bioinformatics Center, University of Copenhagen, DK-2200 Copenhagen, Denmark Corresponding author: jonas...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...recombination, the other two being sperm/egg typing and population phasing. Family-based methods have several advantages: (1) family-based methods capture differences between male and female recombination rates (known to vary substantially throughout the ) (Kong et al. 2010); (2) family-based methods allow us...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...responsible for antigen binding. The IGH locus exhibits high levels of structural variation (SV) and allelic diversity, contributing to significant variability in the germline repertoire within a population and between the haplotypes in the same individual (Rodriguez et al. 2023). During B cell development...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
.... However, the absence of a chromosome-scale, high-contiguity for A. avenae has been a limitation in the -wide identification of gene families potentially involved in desiccation tolerance. In this study, we assemble a high-quality, telomere-to-telomere haplotype of A. avenae. Transcriptomic analyses reveal...
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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
...from Iberia by only eight 1-nt differences (Fig. 2B).Prevalence of Δblock in historical Iberian wolf samplesFor a recent temporal perspective on the prevalence of the dog Δblock in the Iberian wolf population, we analyzed a set of 48 historical Iberian wolf samples spanning periods from 1912 to 2005...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...interpretation of genetic variation and its role in disease (Browning and Browning 2011; Tewhey et al. 2011). Haplotype assemblies are also essential to the study of population structure, genetic diversity, mechanisms of inheritance, and evolution (Douglas et al. 2001; Green et al. 2010; Adey et al. 2013...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...-of-the-art both in terms of species and genomic coverage. The atlas reveals that teleost fishes vary substantially in their retention of duplicated gene copies (ohnologs) since the TGD, which make up 33% of the arowana but only 19% of the cod (Supplemental Table S2). In general, Osteoglossiformes, Otomorpha...

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