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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...Biology, SB RAS, Novosibirsk 630090, Russia; 4Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia; 5Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA; 6China National GeneBank, BGI-Shenzhen, Shenzhen...
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LETTER: A Primary Male Autosomal Linkage Map of the Horse Genome
- Gabriella Lindgren,
- Kaj Sandberg,
- Helena Persson,
- Stefan Marklund,
- Matthew Breen,
- Björn Sandgren,
- Johan Carlstén,
- and Hans Ellegren
Genome Res. September 1, 1998 8: 951-966; doi:10.1101/gr.8.9.951
...genetic and physical map data have been made ( Breen et al. 1997 ; Godard et al. 1997 ). The reasons for the slow progress in equine gene mapping are several and relate mainly to the economy and practice of horse breeding (but potentially also to the fact that the horse in some cases is seen more...
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RESOURCE: The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes
- Bhanu P. Chowdhary,
- Terje Raudsepp,
- Srinivas R. Kata,
- Glenda Goh,
- Lee V. Millon,
- Veronica Allan,
- François Piumi,
- Gérard Guérin,
- June Swinburne,
- Matthew Binns,
- Teri L. Lear,
- Jim Mickelson,
- James Murray,
- Douglas F. Antczak,
- James E. Womack,
- and Loren C. Skow
Genome Res. April 1, 2003 13: 742-751; doi:10.1101/gr.917503
...model ( Rieder et al. 2000 ). The First International Equine Gene Mapping Workshop (October 1995, Lexington, Kentucky, USA) signaled the beginning of an organized equine genomics program. Significant strides have since been made in expanding the gene map of the horse ( Equus caballus; ECA, reviewed...
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LETTER: A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep
- Belinda J. Norris and
- Vicki A. Whan
Genome Res. August 2008 18: 1282-1293; Published in Advance May 20, 2008, doi:10.1101/gr.072090.107
...in these species (data not shown). The Merino ASIP intron and exon sequence data and the INRA BAC clone sequence data were used to search the CHORI Texel sheep library BAC-end sequences to identify BAC clones in the region of the ovine ASIP gene. In addition, the mapping of the full set of sheep BACs to the cow...
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Letter: Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
- Nicolas Di-Poï,
- Juan I. Montoya-Burgos,
- and Denis Duboule
Genome Res. April 2009 19: 602-610; Published in Advance February 18, 2009, doi:10.1101/gr.087932.108
..., for example, within Hoxa3 and Hoxd13 ( Fig. 1A,D ). We examined the exact sizes of Hox gene clusters in other recently released vertebrate s, including those of the dog, horse, platypus, opossum, and zebrafish. As shown in Figure 2 , lizard Hox gene clusters were found comparatively larger than those of all...
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Methods: Haplotype Analysis in Multiple Crosses to Identify a QTL Gene
- Xiaosong Wang,
- Ron Korstanje,
- David Higgins,
- and Beverly Paigen
Genome Res. September 2004 14: 1767-1772; Published in Advance August 12, 2004, doi:10.1101/gr.2668204
...encoded protein, apolipoprotein A-II (APOA2), helps maintain plasma HDL levels in mice (for review, see Blanco-Vaca et al. 2001 ). To determine whether Apoa2 was the Hdlq5 gene, we took the approach of haplotype analysis. Recent single nucleotide polymorphism (SNP) maps indicate that the of common inbred...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
...version: In this window In a new window Figure 1. Identification of satellite-free centromeres in Equus asinus. ChIP-seq reads from primary fibroblasts of HorseS (A) and DonkeyA (B) were mapped on the EquCab2.0 horse reference . Immunoprecipitation was performed with an antibody against human CENPA (red...
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LETTER: Alu-mediated 100-kb deletion in the primate genome: The loss of the agouti signaling protein gene in the lesser apes
- Kazuhiro Nakayama and
- Takafumi Ishida
Genome Res. April 2006 16: 485-490; doi:10.1101/gr.4763906
...) Molecular structure and chromosomal mapping of the human homolog of the agouti gene. Proc. Natl. Acad. Sci. 91 : 9760 – 9764 . ↵ Leeb T. , Doppe A. , Kriegesmann B. , Brenig B. ( 2000 ) Genomic structure and nucleotide polymorphisms of the porcine agouti signaling protein gene (ASIP). Anim. Genet. 31 : 335...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
..., Rush LJ, Alvarez CE. 2009. Mapping DNA structural variation in dogs. Genome Res 19: 500–509. ↵ Chu MX, Liu ZH, Jiao CL, He YQ, Fang L, Ye SC, Chen GH, Wang JY Chu MX, Liu ZH, Jiao CL, He YQ, Fang L, Ye SC, Chen GH, Wang JY. 2007. Mutations in BMPR-IB and BMP-15 genes are associated with litter size...
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Research: Speciation network in Laurasiatheria: retrophylogenomic signals
- Liliya Doronina,
- Gennady Churakov,
- Andrej Kuritzin,
- Jingjing Shi,
- Robert Baertsch,
- Hiram Clawson,
- and Jürgen Schmitz
Genome Res. June 2017 27: 997-1003; Published in Advance March 15, 2017, doi:10.1101/gr.210948.116
...complex ancestral demographic processes. Accumulating reports of discordance between gene and species trees indicate tangled evolutionary histories characterized by character conflicts due to phylogenetic hemiplasy (Avise and Robinson 2008) rather than to methodical errors or differences in taxonomic...

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