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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...in the class II region of the major histocompatibility complex. Nat Genet 29: 217–222. doi:10.1038/ng1001-217 ↵Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen C, Thomas MA, Haussler D, Jacob HJ. 2004. Comparative recombination rates in the rat, mouse, and human s. Genome Res 14: 528–538. doi:10...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
.... However, the sequence information contained in these contigs as well as individual unassembled T. gondii genomic and EST reads (Sanger chemistry) that matched mtDNA from related species, served as a template for PCR primer design that carefully avoided NUMTs (Supplemental Table S1). Mitochondria...
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Research: Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps
- Beth L. Dumont,
- Michael A. White,
- Brian Steffy,
- Tim Wiltshire,
- and Bret A. Payseur
Genome Res. January 2011 21: 114-125; Published in Advance October 26, 2010, doi:10.1101/gr.111252.110
...of linkage maps developed for a subset of the Apis mellifera and Apis florea s, two taxa that diverged ;8–10 million years ago (Mya), yielded similar conclusions (Meznar et al. 2010). The genetic map lengths of orthologous intervals are weakly correlated between human, mouse, and rat (Jensen-Seaman et al...
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ARTICLE: A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome
- Mizuki Ohno,
- Tomofumi Miura,
- Masato Furuichi,
- Yohei Tominaga,
- Daisuke Tsuchimoto,
- Kunihiko Sakumi,
- and Yusaku Nakabeppu
Genome Res. May 2006 16: 567-575; doi:10.1101/gr.4769606
...and mitochondria. Nucleic Acids Res. 28 : 1355 – 1364 . ↵ Rohrer G.A. , Fahrenkrug S.C. , Nonneman D. , Tao N. , Warren W.C. ( 2002 ) Mapping microsatellite markers identified in porcine EST sequences. Anim. Genet. 33 : 372 – 376 . ↵ Romanienko P.J. , Camerini-Otero R.D. ( 2000 ) The mouse Spo11 gene is required...
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LETTER: Exceptionally high levels of recombination across the honey bee genome
- Martin Beye,
- Irene Gattermeier,
- Martin Hasselmann,
- Tanja Gempe,
- Morten Schioett,
- John F. Baines,
- David Schlipalius,
- Florence Mougel,
- Christine Emore,
- Olav Rueppell,
- Anu Sirviö,
- Ernesto Guzmán-Novoa,
- Greg Hunt,
- Michel Solignac,
- and Robert E. Page, Jr.
Genome Res. November 2006 16: 1339-1344; Published in Advance October 25, 2006, doi:10.1101/gr.5680406
...of the honey bee, Apis mellifera , based on RAPD markers . Genetics 139 : 1371 – 1382 . ↵ Jensen-Seaman, M.I. , Furey, T.S. , Payseur, B.A. , Lu, Y. , Roskin, K.M. , Chen, C.F. , Thomas, M.A. , Haussler, D. , Jacob, H.J. ( 2004 ) Comparative recombination rates in the rat, mouse, and human s . Genome Res. 14...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...tool (Lai et al. 2008), with default parameters. For the comparison between Mus musculus and rat and between all four Hominidaes, inter-chromosomal synteny breaks involving genomic regions longer than 3 Mb were identified and selected using the synteny map in Ensembl v82 (Aken et al. 2017).To estimate...
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LETTER: Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome
- Zhengdong Zhang,
- Paula E. Burch,
- Austin J. Cooney,
- Rainer B. Lanz,
- Fred A. Pereira,
- Jiaqian Wu,
- Richard A. Gibbs,
- George Weinstock,
- and David A. Wheeler
Genome Res. April 2004 14: 580-590; doi:10.1101/gr.2160004
...(data not shown). Genomic Distribution of Nuclear Receptors The genomic locations of NRs were mapped onto the rat karyogram ( Fig. 1 ). NR genes were distributed throughout the rat except for chromosomes 9, 12, 14, and 17. Although rat chromosome Y was unavailable, no NR genes are found on the human Y...
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Letter: Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
- Xiyin Wang,
- Haibao Tang,
- John E. Bowers,
- and Andrew H. Paterson
Genome Res. June 2009 19: 1026-1032; Published in Advance April 16, 2009, doi:10.1101/gr.087288.108
...) Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat . Mol. Biol. Evol. 23 : 927 – 940 . ↵ Fu, H. , Zheng, Z. , Dooner, H.K. ( 2002 ) Recombination rates between adjacent genic and retrotransposon regions in maize...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth Christina A. Cuomo 1 , 5 , 6 , Christopher A. Desjardins 1 , 5 , Malina A. Bakowski 2 , 5 , Jonathan Goldberg 1 , Amy T. Ma 2...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...1989 ). This new class of genetic markers was also deployed in the rat. Since then, the rat project has yielded a tremendous wealth of genomic resources including genetic maps; radiation hybrid (RH) cell lines and the associated RH maps (&gt;5000 genetic markers and 19,500 genes and ESTs mapped); c...

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