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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
...trimmed from the reads, adapter sequences were removed, and overlapping read pairs were collapsed using AdapterRemoval v.2.2.0 (Schubert et al. 2016) with default parameters. Reads were mapped to the dog reference CanFam3.1 (Lindblad-Toh et al. 2005) using BWA v.0.7.16a (Li and Durbin 2009...
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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
...-mer-spectra analysis revealed a similar size across all four sequenced individuals (mean size across k-mer sizes 20, 30, and 40: 800–817 Mb) and pointed toward lower estimates of -wide heterozygosity in both offspring (mean heterozygosity across k-mer sizes 20, 30, and 40; wildI: 0.097%, parent: 0.119%, offspring1: 0...
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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
...with annotations of accessible chromatin regions identified using ATAC-seq data from the liver and brain. Analysis of the overlap between TEs and accessible chromatin revealed a large depletion of TEs in accessible chromatin. Although TEs represent ∼52% of the sequence, TE insertions only represent <20...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...specified for each method. The options for the six callers can be found in Supplemental Table S4.Precision and recallFor the samples from TCGA and PCAWG, we used the consensus SNV calls published previously (Ellrott et al. 2018; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) as a truth...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
..., ENSCAFT00000022860, ENSCAFT00000009984; CN below two in many domestic and village dogs) (Fig. 1B) and SLIT2 (Chr 3: 88,965,914–88,966,914; CN below two in many wolves) (Fig. 1C) genes which, in humans, have been associated with adaptation to high altitude and neural development, respectively (Hu 1999...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...Whole- long-read sequencing downsampling and its effect on variant-calling precision and recall William T. Harvey1, Peter Ebert2,3,4, Jana Ebler2,4, Peter A. Audano5, Katherine M. Munson1, Kendra Hoekzema1, David Porubsky1, Christine R. Beck5,6, Tobias Marschall2,4, Kiran Garimella7 and Evan E...
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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
...be used to identify crossovers from family sequencing data.As whole- sequencing (WGS) becomes ubiquitous, large family-based cohorts are now available, which have the potential to reveal more about how genetic material is transmitted within families and about how shared genetic material contributes...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...1983–2014. Until the third founder arrived to the population in 1991, there was at most one pack reproducing per year. Because the first two founders died early (the female founder in 1985), there were two generations of incestuous full-sibs and parent-offspring breeding as revealed from the pedigree...
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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: 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
...An atlas of fish evolution reveals delayed rediploidization following the teleost whole- duplication Elise Parey1,2, Alexandra Louis1, Jérôme Montfort2, Yann Guiguen2, Hugues Roest Crollius1 and Camille Berthelot1,3 1Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de...

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