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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...unsuitable for these complex and repetitive regions of the because they do not make use of the assembly graph or consider multimapped reads. This problem is not unique to human, and other species such as sheep and cattle have many more acrocentric or telocentric chromosomes than human (23 and 29...
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RESEARCH: Low Frequency of Microsatellites in the Avian Genome
- Craig R. Primmer,
- Terje Raudsepp,
- Bhanu P. Chowdhary,
- Anders Pape Møller,
- and Hans Ellegren
Genome Res. May 1, 1997 7: 471-482; doi:10.1101/gr.7.5.471
...the mutational processes involved ( Amos et al. 1996 ; Primmer et al. 1996 ). Such understanding is important for the proper use of microsatellites in evolutionary contexts, for example, for phylogeny reconstruction ( Jarne and Lagoda 1996 ) and also for addressing general questions relating to organization...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...; Eusebi et al. 2020). Many studies compare and utilize different types of marker techniques, including mitochondrial DNA barcoding (mtDNA) (Guo et al. 2006), the Y-Chromosome technique (Bruford et al. 2003), minisatellite and microsatellite markers (Ćurković et al. 2016), and single...
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RESOURCE: An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci
- Jillian F. Maddox,
- Kizanne P. Davies,
- Allan M. Crawford,
- Dennis J. Hulme,
- Daniel Vaiman,
- Edmond P. Cribiu,
- Bradley A. Freking,
- Ken J. Beh,
- Noelle E. Cockett,
- Nina Kang,
- Christopher D. Riffkin,
- Roger Drinkwater,
- Stephen S. Moore,
- Ken G. Dodds,
- Joanne M. Lumsden,
- Tracey C. van Stijn,
- Sin H. Phua,
- David L. Adelson,
- Heather R. Burkin,
- Judith E. Broom,
- Johannes Buitkamp,
- Lisa Cambridge,
- William T. Cushwa,
- Emily Gerard,
- Susan M. Galloway,
- Blair Harrison,
- Rachel J. Hawken,
- Stefan Hiendleder,
- Hannah M. Henry,
- Juan F. Medrano,
- Korena A. Paterson,
- Laurent Schibler,
- Roger T. Stone,
- and Beryl van Hest
Genome Res. July 1, 2001 11: 1275-1289; Published in Advance June 12, 2001, doi:10.1101/gr.135001
...and size correlation between the scoring for these two microsatellites. View larger version: In this window In a new window Figure 1. An updated genetic linkage map for the sheep. Loci shown on the main framework map were positioned with odds of &gt;1000 : 1. Loci to the right of the main framework map...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...mammals, located in the GTL2-DLK1 intergenic region, that—in wild-type sheep—suppresses postnatal muscular expression of a cluster of imprinted genes (including the paternally expressed DLK1 and PEG11 genes). Animals inheriting this mutation from their sire express the callipyge muscular hypertrophy...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...recombination rate is expected to lead to reduced genetic variation via background selection (loss of neutral variants linked to deleterious mutations during purifying selection) (Charlesworth 1994; Comeron 2017) and selective sweeps/hitch-hiking (haplotypes around advantageous mutations increase in frequency...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...the previously recognized microsatellite, single-nucleotide polymorphism (SNP), and short insertion/deletion (indel) variants. SVs can take the form of deletions, insertions, and duplications (commonly grouped under the term copy number variation [CNV]), as well as inversions and translocations, which have been...
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LETTER: Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
- Mikael Brandström and
- Hans Ellegren
Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
...estimates of gene flow and genetic differentiation ( Adams et al. 2004 ; Curtu et al. 2004 ). Brohede and Ellegren (1999) analyzed a number of sheep and ovine microsatellite orthologs and found a tendency for point mutations to be enriched in microsatellite ends and in the immediate microsatellite flanking...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...), possibly because of increased mutation frequency associated with DSBs. It is also well known that chromosomal inversions result in suppressed regional recombination when heterozygous (Sturtevant 1921; Jaarola et al. 1998), a proposed mechanism by which speciation arises in the presence of gene flow (Noor...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
...of exon 6 in the Miniature (Fig. 5A,B) and Shagya Arabian (data not shown). Exon 6 consists of an array of imperfect tandem repeats (Fig. 5C,D) and represents the repeat domain of the PMEL protein (Hoashi et al. 2006). An autosomal dominant C>T missense mutation in exon 11 changes the second amino acid...

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