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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
.... All samples were then sequenced on Illumina HiSeq 2000 instruments, using the 2 × 100-bp paired-end protocol, by the GIGA Genomics platform (University of Liège). The sequence data were mapped using BWA-MEM 0.7.5a (Li 2013) to bovine reference ARS-UCD1.2. Afterward, SAMtools 1.9 (Li and Durbin 2009...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...map spl-TRs in a -wide manner across tissues throughout the whole body by using the Genotype-Tissue expression (GTEx) v8 data set, a population-scale resource of whole- sequencing (WGS) and RNA sequencing (RNA-seq).ResultsGenome-wide identification of spl-TRs across 49 tissuesWe discovered cis spl...
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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
...in populations by screens to utilizing and cloning QTLs, it is important to have dense marker maps for livestock. The most recently published sheep linkage map, termed the second generation map, comprised 512 loci with an average spacing of 6 cM ( de Gortari et al. 1998 ). However, many of the markers used...
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LETTER: A Primary Male Autosomal Linkage Map of the Horse Genome
- Gabriella Lindgren,
- Kaj Sandberg,
- Helena Persson,
- Stefan Marklund,
- Matthew Breen,
- Björn Sandgren,
- Johan Carlstén,
- and Hans Ellegren
Genome Res. September 1, 1998 8: 951-966; doi:10.1101/gr.8.9.951
....L. , Beattie C.W. ( 1997 ) A second-generation linkage map of the bovine . Genome Res. 7 : 235 – 249 . ↵ Lear T.L. , Irwin Z. , Brandon R. , Bell K. , Mathiason K. , Bailey E. ( 1998 ) Physical assignment of microsatellite markers to horse chromosomes using FISH. Proceedings, plant and animal VI , p 162...
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ARTICLE: Extensive Genome-wide Linkage Disequilibrium in Cattle
- Frédéric Farnir,
- Wouter Coppieters,
- Juan-José Arranz,
- Paulette Berzi,
- Nadine Cambisano,
- Bernard Grisart,
- Latifa Karim,
- Fabienne Marcq,
- Laurence Moreau,
- Myriam Mni,
- Carine Nezer,
- Patricia Simon,
- Pascal Vanmanshoven,
- Danny Wagenaar,
- and Michel Georges
Genome Res. February 1, 2000 10: 220-227; doi:10.1101/gr.10.2.220
.... Appl. Genet. 38 : 226 – 231 . ↵ Kappes S.M. , Keele J.W. , Stone R.T. , McGraw R.A. , Sonstegard T.S. , Smith T.P.L. , Lopez-Corrales N.L. , Beattie C.W. ( 1997 ) A second-generation linkage map of the bovine . Genome Res. 7 : 235 – 249 . ↵ Kruglyak L. ( 1999 ) Prospects for whole- linkage...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...chromosome coordinates using the UCSC Genome Browser liftOver tool (Kent et al. 2002) with a minimum ratio of remapped bases >0.1. For each BAC clone mapped to the chicken chromosomes, various genomic features selected to estimate the probability of clones to hybridizewithmetaphase chromosomes in distant...
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RESOURCE: A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites
- Naoya Ihara,
- Akiko Takasuga,
- Kazunori Mizoshita,
- Haruko Takeda,
- Mayumi Sugimoto,
- Yasushi Mizoguchi,
- Takashi Hirano,
- Tomohito Itoh,
- Toshio Watanabe,
- Kent M. Reed,
- Warren M. Snelling,
- Steven M. Kappes,
- Craig W. Beattie,
- Gary L. Bennett,
- and Yoshikazu Sugimoto
Genome Res. October 2004 14: 1987-1998; doi:10.1101/gr.2741704
...resolution of 0.8 cM at the 95% confidence level (∼800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (&gt;3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-c...
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ARTICLE: A linkage map of the ovine X chromosome.
- S M Galloway,
- V Hanrahan,
- K G Dodds,
- M D Potts,
- A M Crawford,
- and D F Hill
Genome Res. August 1996 6: 667-677; doi:10.1101/gr.6.8.667
...Crawford, A M S Galloway Hanrahan Hill, DF M.D. Potts K G, Dodds D Hill Hanrahan V Crawford, AM Dodds, K V, Hanrahan MD Potts 10.1101/gr.6.8.667 1088-9051 genome;6/8/667 A linkage map of the ovine X chromosome. A linkage map of the ovine X chromosome. S M Galloway , V Hanrahan , K G Dodds , M D Potts , A M...
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RESOURCE: A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence
- Denis M. Larkin,
- Annelie Everts-van der Wind,
- Mark Rebeiz,
- Peter A. Schweitzer,
- Sharon Bachman,
- Cheryl Green,
- Chris L. Wright,
- Edhilvia J. Campos,
- Leslie D. Benson,
- Jennifer Edwards,
- Lei Liu,
- Kazutoyo Osoegawa,
- James E. Womack,
- Pieter J. de Jong,
- and Harris A. Lewin
Genome Res. August 2003 13: 1966-1972; doi:10.1101/gr.1560203
...of the mouse . Nature 418 : 743 -750. ↵ Kappes, S.M., Keele, J.W., Stone, R.T., McGraw, R.A., Sonstegard, T.S., Smith, T.P., Lopez-Corrales, N.L., and Beattie, C.W. 1997 . A second-generation linkage map of the bovine . Genome Res. 7 : 235 -249. ↵ Kumar, S. and Hedges, S.B. 1998 . A molecular timescale...
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RESOURCE: A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
- Annelie Everts-van der Wind,
- Srinivas R. Kata,
- Mark R. Band,
- Mark Rebeiz,
- Denis M. Larkin,
- Robin E. Everts,
- Cheryl A. Green,
- Lei Liu,
- Shreedhar Natarajan,
- Tom Goldammer,
- Jun Heon Lee,
- Stephanie McKay,
- James E. Womack,
- and Harris A. Lewin
Genome Res. July 2004 14: 1424-1437; doi:10.1101/gr.2554404
....M., Keele, J.W., Stone, R.T., McGraw, R.A., Sonstegard, T.S., Smith, T.P., Lopez-Corrales, N.L., and Beattie, C.W. 1997 . A second-generation linkage map of the bovine . Genome Res. 7 : 235 –249. ↵ Larkin, D.M., Serov, O.L., Borodin, P.M., Zhdanova, N.S., and Searle, J.B. 2000 . Comparative mapping...

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