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Method: High-throughput single-molecule telomere characterization
- Jennifer McCaffrey,
- Eleanor Young,
- Katy Lassahn,
- Justin Sibert,
- Steven Pastor,
- Harold Riethman,
- and Ming Xiao
Genome Res. November 2017 27: 1904-1915; Published in Advance October 12, 2017, doi:10.1101/gr.222422.117
...identity) segmental duplications, large structural variations, and reference sequence gaps and misassemblies (Stong et al. 2014). While most SRE regions are 40–150 kb in size, long SRE regions of up to ∼300 kb have been identified in a few subtelomeres, including 1p, 8p, and 5q. Motif-dependent nick...
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Method: Genome-wide characterization of centromeric satellites from multiple mammalian genomes
- Can Alkan,
- Maria Francesca Cardone,
- Claudia Rita Catacchio,
- Francesca Antonacci,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Stefania Purgato,
- Monica Zoli,
- Giuliano Della Valle,
- Evan E. Eichler,
- and Mario Ventura
Genome Res. January 2011 21: 137-145; Published in Advance November 16, 2010, doi:10.1101/gr.111278.110
...:137–145 2011 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/11; www..org Genome Research 137 www..org assemblies (Eichler et al. 2004; Rudd and Willard 2004). In fact, in each chromosome assembly there is no sequence in the existing gap between the p and q arms (Rudd and Willard 2004). However, a few...
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LETTER: A Fine Physical Map of the Rice Chromosome 4
- Qiang Zhao,
- Yu Zhang,
- Zhukuan Cheng,
- Mingsheng Chen,
- Shengyue Wang,
- Qi Feng,
- Yucheng Huang,
- Ying Li,
- Yesheng Tang,
- Bo Zhou,
- Zhehua Chen,
- Shuliang Yu,
- Jingjie Zhu,
- Xin Hu,
- Jie Mu,
- Kai Ying,
- Pei Hao,
- Lei Zhang,
- Yiqi Lu,
- Lei S. Zhang,
- Yilei Liu,
- Zhen Yu,
- Danlin Fan,
- Qijun Weng,
- Ling Chen,
- Tingting Lu,
- Xiaohui Liu,
- Peixin Jia,
- Tongguo Sun,
- Yongrui Wu,
- Yujun Zhang,
- Ying Lu,
- Can Li,
- Rong Wang,
- Haiyan Lei,
- Tao Li,
- Hao Hu,
- Mei Wu,
- Runquan Zhang,
- Jianping Guan,
- Jia Zhu,
- Gang Fu,
- Minghong Gu,
- Guofan Hong,
- Yongbiao Xue,
- Rod Wing,
- Jiming Jiang,
- and Bin Han
Genome Res. May 1, 2002 12: 817-823; doi:10.1101/gr.48902
...coverage of 89% ( Chen et al. 2002 ). The chromosome 4 map had a coverage of 87.7% with 23 gaps ( Chen et al., 2002 ). As part of the IRGSP effort to sequence the rice , we have made an effort to construct a sequence-ready Nipponbare chromosome 4 physical map. Because O. sativa indica and japonica...
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ARTICLE: Fine-Resolution Physical Mapping of Genomic Diversity in Candida albicans
- Hiroji Chibana,
- Janna L. Beckerman,
- and P.T. Magee
Genome Res. December 1, 2000 10: 1865-1877; doi:10.1101/gr.148600
...on chromosome 7, it seemed possible that variations in the MRS might contribute significantly to the CLP of chromosome 7. To measure the size of the gaps between the Sfi I fragments 7A-7F and 7F-7G, the genomic DNA was digested with the enzyme Xho I, which does not cut in the MRS of chromosome 7. The fragments...
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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
...and therefore do not faithfully represent HindIII restriction site sequences or actual restriction fragment sizes. Thus, we expect that in silico coordinates derived from regions of the assembly containing gaps would have a negative impact on the concordance between BAC-end sequence coordinates and in silico...
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ARTICLE: Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.
- R A Macina,
- K Morii,
- X L Hu,
- D G Negorev,
- C Spais,
- L A Ruthig,
- and H C Riethman
Genome Res. October 1995 5: 225-232; doi:10.1101/gr.5.3.225
.... Long-range mapping of gaps and telomeres with RecA-assisted restriction endonuclease (RARE) cleavage. Nature Genet. 6 : 379 – 383 . Gnirke, A., , Huxley, C. , Peterson, K. , Olson M.V. Gnirke, A., Huxley, C. Peterson, K. and Olson M.V. 1993 . Microinjection of intact 200 to 500 kb fragments of YAC DNA...
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LETTER: Analysis of 5S rDNA Arrays in Arabidopsis thaliana: Physical Mapping and Chromosome-Specific Polymorphisms
- C. Cloix,
- S. Tutois,
- O. Mathieu,
- C. Cuvillier,
- M.C. Espagnol,
- G. Picard,
- and S. Tourmente
Genome Res. May 1, 2000 10: 679-690; doi:10.1101/gr.10.5.679
...and colocalize partly with 5S rDNA in chromosomes 3, 4, and 5. Mozo et al. (1999) have established a complete BAC-based physical map of the Arabidopsis , but gaps remain at centromeres and 5S locus. Previously, we ( Tutois et al. 1999 ) have established an ∼1000-kb physical map of the chromosome 5...
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RESOURCE: Toward a Cytological Characterization of the Rice Genome
- Zhukuan Cheng,
- C. Robin Buell,
- Rod A. Wing,
- Minghong Gu,
- and Jiming Jiang
Genome Res. December 1, 2001 11: 2133-2141; doi:10.1101/gr.194601
...physical characterization of the large linkage gaps will be of critical importance in the acceleration of the International Rice Genome Sequencing Project. METHODS Materials O. sativa spp. japonica rice var. Nipponbare and O. sativa spp. indica rice var. Zhongxian 3037 were used for cytological studies...
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LETTER: Physical and Comparative Mapping of Distal Mouse Chromosome 16
- Deborah E. Cabin,
- Jennifer W. McKee-Johnson,
- Lydia E. Matesic,
- Tim Wiltshire,
- Elizabeth E. Rue,
- Anne E. Mjaatvedt,
- Yong Kang Huo,
- Julie R. Korenberg,
- and Roger H. Reeves
Genome Res. September 1, 1998 8: 940-950; doi:10.1101/gr.8.9.940
...of the fragmentation intervals to which they mapped except when clone size constraints gave a better localization within an interval. End clones were most useful in aligning YACs because they define the ends of precisely sized intervals. The only gap in YAC coverage falls between YACs I103E5 and 183G11, and is crossed...
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LETTER: A Physical Map of the Leishmania majorFriedlin Genome
- Alasdair C. Ivens,
- Sharon M. Lewis,
- Azadeh Bagherzadeh,
- Linglan Zhang,
- Ho M. Chan,
- and Deborah F. Smith
Genome Res. February 1, 1998 8: 135-145; doi:10.1101/gr.8.2.135
...that stretch contiguously from telomere to telomere. Although it is difficult at this stage to generate accurate figures for the physical extent of the presumed gaps, these could be determined hypothetically by restriction enzyme mapping. In addition, the need for gap closure has initiated a number...

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