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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
...-scale investigation of recombination rate variation across the equine , as historical recombination rates can be estimated by coalescent analysis of linkage disequilibrium (LD) patterns in high-density SNP data (Auton and McVean 2007). These estimates can help identify putative recombination hotspots and compare...
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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
...) of these features revealed that a majority of SV were enriched (Log2(Fold Enrichment) > 0) in nongenic gene deserts, intergenic regions, or pseudogenes and not predicted to disrupt genomic regions associated with gene function. Relatively few SV were identified within regulatory elements (e.g., promoters, enhancers...
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Research: The recombination landscape of the zebra finch Taeniopygia guttata genome
- Niclas Backström,
- Wolfgang Forstmeier,
- Holger Schielzeth,
- Harriet Mellenius,
- Kiwoong Nam,
- Elisabeth Bolund,
- Matthew T. Webster,
- Torbjörn Öst,
- Melanie Schneider,
- Bart Kempenaers,
- and Hans Ellegren
Genome Res. April 2010 20: 485-495; Published in Advance March 31, 2010, doi:10.1101/gr.101410.109
...(Groenen et al. 2009), mouse and human (Jensen-Seaman et al. 2004). Table 1. Mean recombination rate (cM/Mb) in distal (<15 Mb from chromosome end) and central parts (>15 Mb from chromosome end) of chromosomes larger than 50 Mb in four vertebrates with available high-density linkage map and draft sequence...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...-J, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM,Wong GK-S, et al. 2009. A highdensity SNP-based linkage map of the chicken reveals sequence features correlated with recombination rate. Genome Res 19: 510–519. Hansson B, Ljungqvist M, Dawson DA, Mueller JC, Olano-Marin J, Ellegren H, Nilsson JA. 2009. Avian...
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Research: Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
- Naveen Kumar Kadri,
- Chad Harland,
- Pierre Faux,
- Nadine Cambisano,
- Latifa Karim,
- Wouter Coppieters,
- Sébastien Fritz,
- Erik Mullaart,
- Denis Baurain,
- Didier Boichard,
- Richard Spelman,
- Carole Charlier,
- Michel Georges,
- and Tom Druet
Genome Res. October 2016 26: 1323-1332; Published in Advance August 11, 2016, doi:10.1101/gr.204214.116
...Database reports at least 37 genes related to reciprocal meiotic recombination in humans (Supplemental Table S1) (e.g., Baudat et al. 2013). Genealogies have been genotyped at high density for different purposes, including the study of complex diseases in humans or genomic selection in animals and plants...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...high-density linkage map of the collared flycatcher (Kawakami et al. 2014a, b) enabled us to examine the relationship between recombination and differentiation in more detail than previously possible. Lineage-specific differentiation (PBS) significantly increased with decreasing recombination rate...
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Research: Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
- Martin Völker,
- Niclas Backström,
- Benjamin M. Skinner,
- Elizabeth J. Langley,
- Sydney K. Bunzey,
- Hans Ellegren,
- and Darren K. Griffin
Genome Res. April 2010 20: 503-511; Published in Advance March 31, 2010, doi:10.1101/gr.103663.109
...linkage map of the chicken reveals sequence features correlated with recombination rate. Genome Res 19: 510–519. Gu W, Zhang F, Lupski JR. 2008. Mechanisms for human genomic rearrangements. Pathogenetics 1: 4. doi: 10.1186/1755-8417-1-4. Hale MC, Jensen H, Birkhead TR, Burke T, Slate J. 2008. A comparison...
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Methods: Two-parameter characterization of chromosome-scale recombination rate
- Wentian Li and
- Jan Freudenberg
Genome Res. December 2009 19: 2300-2307; Published in Advance September 14, 2009, doi:10.1101/gr.092676.109
...: 1071–1078. Grigoriev A. 1998. Analyzing s with cumulative skew diagrams. Nucleic Acids Res 26: 2286–2290. Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans R, Besnier F, Lathrop M, Muir WM, Wong GKS, et al. 2009. A high density SNP based linkage map of the chicken reveals sequence...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
..., Santa Cruz, California 95064, USA; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; 4Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Corresponding authors: jcahill@rockefeller.edu, ejarvis@rockefeller.eduAbstractVocal learning, the ability...
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