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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...this goal, we set up haplotype tests to trace the segments involved in the rearrangements through generations, taking into account various Figure 2. Validation of 12 IRs by cytogenetic analyses. (A) FISH mapping on cultured fibroblasts from four daughters of Nt with BAC clones located in the translocated...
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Resource: A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons
- Oronzo Capozzi,
- Lucia Carbone,
- Roscoe R. Stanyon,
- Annamaria Marra,
- Fengtang Yang,
- Christopher W. Whelan,
- Pieter J. de Jong,
- Mariano Rocchi,
- and Nicoletta Archidiacono
Genome Res. December 2012 22: 2520-2528; Published in Advance August 14, 2012, doi:10.1101/gr.138651.112
...), Symphalangus (2n = 50), and Nomascus (2n = 52). Molecular cytogenetic techniques now allow a significantly higher resolution than chromosome painting through the use of hybridization of precisely mapped BAC clones, microarrays, and selective sequencing. Using these approaches we recently defined...
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Research: Small chromosomal regions position themselves autonomously according to their chromatin class
- Harmen J.G. van de Werken,
- Josien C. Haan,
- Yana Feodorova,
- Dominika Bijos,
- An Weuts,
- Koen Theunis,
- Sjoerd J.B. Holwerda,
- Wouter Meuleman,
- Ludo Pagie,
- Katharina Thanisch,
- Parveen Kumar,
- Heinrich Leonhardt,
- Peter Marynen,
- Bas van Steensel,
- Thierry Voet,
- Wouter de Laat,
- Irina Solovei,
- and Boris Joffe
Genome Res. June 2017 27: 922-933; Published in Advance March 24, 2017, doi:10.1101/gr.213751.116
...(MMU3) (B) visualized by the UCSC Genome Browser. The sequence features of the chromosomal loci indicated by red open rectangles in the chromosome ideograms are viewed below the ideograms. Tracks, ordered from top to bottom, are: genes, TADs, BACs used for fluorescence in situ hybridization (FISH...
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RESOURCE: Human Genome Anatomy: BACs Integrating the Genetic and Cytogenetic Maps for Bridging Genome and Biomedicine
- Julie R. Korenberg,
- Xiao-Ning Chen,
- Zhiguang Sun,
- Zheng-Yang Shi,
- Shaowu Ma,
- Eddy Vataru,
- Dean Yimlamai,
- Jean S. Weissenbach,
- Hiroaki Shizuya,
- Melvin I. Simon,
- Sebastian S. Gerety,
- Huy Nguyen,
- Irina S. Zemsteva,
- Lester Hui,
- James Silva,
- Xiaoyun Wu,
- Bruce W. Birren,
- and Thomas J. Hudson
Genome Res. October 1, 1999 9: 994-1001; doi:10.1101/gr.9.10.994
...STSs, including 642 polymorphic markers and 957 bacterial artificial chromosomes (BACs), each of which was localized on high resolution fluorescent banded chromosomes. These BACs constitute a resource that bridges map levels and provides the tools to seamlessly translate questions raised by genomic...
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RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
- Eiichi Shoguchi,
- Takeshi Kawashima,
- Yutaka Satou,
- Makoto Hamaguchi,
- Tadasu Sin-I,
- Yuji Kohara,
- Nik Putnam,
- Daniel S. Rokhsar,
- and Nori Satoh
Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
...cytogenetic characterization of all 14 pairs of C. intestinalis chromosomes, as well as initial large-scale mapping of genomic sequences onto chromosomes by fluorescent in situ hybridization (FISH). Two-color FISH using 170 bacterial artificial chromosome (BAC) clones and construction of joined scaffolds...
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RESOURCE: “KARIBIN,” an Information Resource for Obtaining Genomic Information in a Cytogenetic Band
- Jinghui Zhang,
- Grace Shen-Ong,
- and Jim Ostell
Genome Res. January 1, 1999 9: 91-98; doi:10.1101/gr.9.1.91
...), and bacterial artificial chromosomes (BACs), known disease gene phenotypes, and sequencing status of the region. Genome Data Integration Genetic, phyiscal, and cytogenetic maps are integrated with an STS-mediated approach (Fig. 1 ). Alignments of the various genetic and physical maps are established using...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...the proximal 45 kb of the human Yp11.1/Yp11.2 region maps to proximal chimpanzee Yp11.2 (NW_001252921). This distribution pattern is akin to the FISH signal pattern seen after hybridization of the BAC clones encompassing the human Yp11.2/Yp11.1 region to the chimpanzee Y chromosome ( Fig. 3 ; Supplemental Fig...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
.... Syntenic map A map summarizing the syntenic regions between D. pseudoobscura and D. melanogaster is extremely useful in the identification of orthologous genes, for the identification of chromosomal rearrangements, and the seeding of alignments. As protein sequences provided more robust similarity signals...
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RESOURCE: Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
- Martin Krzywinski,
- John Wallis,
- Claudia Gösele,
- Ian Bosdet,
- Readman Chiu,
- Tina Graves,
- Oliver Hummel,
- Dan Layman,
- Carrie Mathewson,
- Natasja Wye,
- Baoli Zhu,
- Derek Albracht,
- Jennifer Asano,
- Sarah Barber,
- Mabel Brown-John,
- Susanna Chan,
- Steve Chand,
- Alison Cloutier,
- Jonathon Davito,
- Chris Fjell,
- Tony Gaige,
- Detlev Ganten,
- Noreen Girn,
- Kurtis Guggenheimer,
- Heinz Himmelbauer,
- Thomas Kreitler,
- Stephen Leach,
- Darlene Lee,
- Hans Lehrach,
- Michael Mayo,
- Kelly Mead,
- Teika Olson,
- Pawan Pandoh,
- Anna-Liisa Prabhu,
- Heesun Shin,
- Simone Tänzer,
- Jason Thompson,
- Miranda Tsai,
- Jason Walker,
- George Yang,
- Mandeep Sekhon,
- LaDeana Hillier,
- Heike Zimdahl,
- Andre Marziali,
- Kazutoyo Osoegawa,
- Shaying Zhao,
- Asim Siddiqui,
- Pieter J. de Jong,
- Wes Warren,
- Elaine Mardis,
- John D. McPherson,
- Richard Wilson,
- Norbert Hübner,
- Steven Jones,
- Marco Marra,
- and Jacqueline Schein
Genome Res. April 2004 14: 766-779; doi:10.1101/gr.2336604
...; Yokoi et al. 2002 ; Olofsson et al. 2003 ). Here, we describe the creation of major new resources for genomic studies in the rat: (1) the construction of a bacterial artificial chromosome (BAC) fingerprint map spanning the rat ; (2) the construction of a yeast artificial chromosome (YAC) map covering...
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Chicken Special/Resources: Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates
- Wendy A. Kellner,
- Robert T. Sullivan,
- Brian H. Carlson,
- and James W. Thomas
Genome Res. January 2005 15: 166-173; Published in Advance December 8, 2004, doi:10.1101/gr.3066805
...of targeted chromosomal segments that is independent and complementary to whole-genome sequencing. However, at the present time, no complementary resource exists for the efficient targeted physical mapping of the majority of these BAC libraries. Universal overgo-hybridization probes, designed from regions...

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