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Research: Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome
- Erik Axelsson,
- Matthew T. Webster,
- Abhirami Ratnakumar,
- The LUPA Consortium,
- Chris P. Ponting,
- and Kerstin Lindblad-Toh
Genome Res. January 2012 22: 51-63; Published in Advance October 17, 2011, doi:10.1101/gr.124123.111
...by hotspots that are exceptionally long-lived. Results Death of canid PRDM9 We resequenced exon 7 of PRDM9 in representatives from 15 different dog breeds (see Methods) to investigate whether they carry the same two frameshift mutations observed in the publicly available boxer assembly (Supplemental Fig. S1...
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Letter: Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
- Denis M. Larkin,
- Greg Pape,
- Ravikiran Donthu,
- Loretta Auvil,
- Michael Welge,
- and Harris A. Lewin
Genome Res. May 2009 19: 770-777; Published in Advance April 2, 2009, doi:10.1101/gr.086546.108
...of the evolutionary forces that affect genome architecture, synteny relationships among 10 amniotes (human, chimp, macaque, rat, mouse, pig, cattle, dog, opossum, and chicken) were compared at &lt;1 human-Mbp resolution. Homologous synteny blocks (HSBs; N = 2233) and chromosome evolutionary breakpoint regions (EBRs...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...and Robertson 1966 ). Because most nonsynonymous mutations are deleterious, this would tend to increase purifying selection. A higher recombination rate in the marsupial X chromosome and subtelomeric regions might then explain the reduced d N /d S among Monodelphis orthologs from these regions, as well as among...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...positioning of chromosomes during cell division and breakage owing to shearing or mechanical stresses. Genome elimination has been achieved by crossing lines carrying point CENH3 mutations in Arabidopsis (Karimi-Ashtiyani et al. 2015; Kuppu et al. 2015), by -editing to produce frameshifts in CENH3 tail...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
...) with a single exception: The second segment from chromosome 10 is identified as an isolated chromosome by us and is tentatively assigned as 10p + 12a + 22a by Table 1A. The statistics of the breakpoint graph of the mouse, rat, dog, macaque, human, and chimpanzee s Multi-colors Multi-edges Simple vertices Simple...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...probability of being aCFSs. Moreover, the farther away from the centromere, the higher is the breakage frequency of aCFSs. Several genomic contexts/features are known to vary along the length of a chromosome, creating a change in genomic landscape that affects the rates of various mutational events (Hardison...
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Methods: Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
...approaches to whole phylogenetic analysis . Brief. Bioinform. 4 : 63 – 74 . ↵ Webber, C. , Ponting, C.P. ( 2005 ) Hotspots of mutation and breakage in dog and human chromosomes . Genome Res. 15 : 1787 – 1797 . ↵ Wienberg, J. ( 2004 ) The evolution of eutherian chromosomes . Curr. Opin. Genet. Dev. 14 : 657...
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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
...events are concentrated in relatively narrow chromosomal regions, referred to as recombination hotspots (Arnheim et al. 2003). In addition, the recombination rate has been shown to co-vary with several sequence characteristics, in particular the GC-content (Birdsell 2002; International Chicken Genome...
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LETTER: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions
- Eva Darai-Ramqvist,
- Agneta Sandlund,
- Stefan Müller,
- George Klein,
- Stefan Imreh,
- and Maria Kost-Alimova
Genome Res. March 2008 18: 370-379; Published in Advance January 29, 2008, doi:10.1101/gr.7010208
...30 were involved in unbalanced translocations, 14 in interstitial deletions, seven in duplications, one in balanced translocations, and two in insertions (Supplement 4). We differentiated cell lines according to chromosome breakage frequency (Supplement 5). The first group (UOK125, KH39, and UOK115...
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Commentary: Every genome sequence needs a good map
- Harris A. Lewin,
- Denis M. Larkin,
- Joan Pontius,
- and Stephen J. O'Brien
Genome Res. November 2009 19: 1925-1928; Published in Advance July 13, 2009, doi:10.1101/gr.094557.109
..., and their peers conjured the first gene maps nearly a century ago.More recently, linkage, radiationhybrid (RH), bacterial artificial chromosome (BAC), and/or ZOOFISH maps of human, macaque, mouse, rat, dog, cat, horse, opossum, and cattle anchored the sequence assemblies for those species (Table 1). Because...

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