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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 usually varies considerably across chromosomes and genomic regions, and mapping this variation may shed light on the mechanistic control of where recombination is initiated. The reasons for such regional recombination rate variation have been studied in detail in a few organism groups...
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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
...genes and QTL analysis The physical positions of 8217 rice QTLs were downloaded from Gramene (www.gramene.org), covering nine categories and 237 QTL traits. Only QTLs <500K nt were further analyzed, and 3468 QTLs were gained. To examine PAC distributions, PACs across tissues were mapped to these 3468...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...in Table 2. The assembled M. caroli chromosomes do not exhibit any large inter-chromosomal rearrangements with respect to the M. musculus , which was expected from physical maps as well as chromosome paintings (Thybert et al. 2018). However, we detected a large cluster of inversions in Chromosome 17 of ∼5...
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Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- Nicholas H. Putnam,
- Brendan L. O'Connell,
- Jonathan C. Stites,
- Brandon J. Rice,
- Marco Blanchette,
- Robert Calef,
- Christopher J. Troll,
- Andrew Fields,
- Paul D. Hartley,
- Charles W. Sugnet,
- David Haussler,
- Daniel S. Rokhsar,
- and Richard E. Green
Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
...pairs that map reliably to the but span distances >500 kbp or map to different chromosomes. For these libraries, we estimated the noise rate to be approximately one spurious link between unrelated 500-kbp genomic windows (mean of 0.97 such links). The linkage data span various size ranges...
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LETTER: Physical Map and Organization of Chromosome 7 in the Rice Blast Fungus, Magnaporthe grisea
- Heng Zhu,
- Barbara P. Blackmon,
- Maciek Sasinowski,
- and Ralph A. Dean
Genome Res. August 1, 1999 9: 739-750; doi:10.1101/gr.9.8.739
...Physical Map and Organization of Chromosome 7 in the Rice Blast Fungus, Magnaporthe grisea Heng Zhu 1 , 2 , Barbara P. Blackmon 1 , 2 , Maciek Sasinowski 2 , and Ralph A. Dean 1 , 2 , 3 1Department of Plant Pathology...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome Jakob Skou Pedersen 1 , 14 , 15 , Eivind Valen 2 , 3 , 14 , Amhed M. Vargas Velazquez 4 , Brian J. Parker 3 , Morten Rasmussen 4 , 5 , Stinus...
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RESOURCE: A BAC-Based Physical Map of the Chicken Genome
- Chengwei Ren,
- Mi-Kyung Lee,
- Bo Yan,
- Kejiao Ding,
- Bettye Cox,
- Michael N. Romanov,
- Jennifer A. Price,
- Jerry B. Dodgson,
- and Hong-Bin Zhang
Genome Res. December 2003 13: 2754-2758; doi:10.1101/gr.1499303
...., Islam-Faridi, M.N., Scheuring, C., Wang, B., Stelly, D.M., and Zhang, H.-B. 2001 . BAC-based physical map of the rice constructed by restriction fingerprint analysis. Genetics 158 : 1711 -1724. ↵ Waddington, D., Springbett, A.J., and Burt, D.W. 2000 . A chromosome based model to estimate the number...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...High-resolution mapping of open chromatin in the rice genome Wenli Zhang 1 , 4 , Yufeng Wu 1 , 4 , James C. Schnable 2 , Zixian Zeng 1 , Michael Freeling 2 , Gregory E. Crawford 3 and Jiming Jiang 1 , 5...
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LETTER: Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Genome Res. September 2005 15: 1284-1291; Published in Advance August 18, 2005, doi:10.1101/gr.3869505

...known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara , with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged ∼10,000 years ago...
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RESOURCE: A Sequence-Based Integrated Map of Chromosome 22
- William J. Tapper,
- Newton E. Morton,
- Ian Dunham,
- Xiayi Ke,
- and Andrew Collins
Genome Res. July 1, 2001 11: 1290-1295; doi:10.1101/gr.161301
...of the euchromatic portion of 22 has been overestimated by top-down approaches, although as yet the contribution of 22p and q11.1 is not known. Reliable fine-scale mapping could not be achieved by any of the techniques of linkage, radiation hybrids, and cytogenetical assignment, but knowledge of the precise order...

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