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  • 1
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    Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-26
    Description: The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murphy, William J -- Larkin, Denis M -- Everts-van der Wind, Annelie -- Bourque, Guillaume -- Tesler, Glenn -- Auvil, Loretta -- Beever, Jonathan E -- Chowdhary, Bhanu P -- Galibert, Francis -- Gatzke, Lisa -- Hitte, Christophe -- Meyers, Stacey N -- Milan, Denis -- Ostrander, Elaine A -- Pape, Greg -- Parker, Heidi G -- Raudsepp, Terje -- Rogatcheva, Margarita B -- Schook, Lawrence B -- Skow, Loren C -- Welge, Michael -- Womack, James E -- O'brien, Stephen J -- Pevzner, Pavel A -- Lewin, Harris A -- N01-CO-12400/CO/NCI NIH HHS/ -- R01CA-92167/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):613-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA. wmurphy@cvm.tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16040707" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cats/genetics ; Cattle/genetics ; Centromere/genetics ; Chromosomal Instability ; Chromosome Aberrations ; *Chromosome Breakage ; Chromosome Inversion ; Chromosome Mapping ; Chromosomes, Human/genetics ; Chromosomes, Mammalian/*genetics ; Computational Biology ; Dogs/genetics ; *Evolution, Molecular ; *Genome ; Genome, Human ; Horses/genetics ; Humans ; Mammals/*genetics ; Mice/genetics ; Neoplasms/genetics ; Rats/genetics ; Swine/genetics ; *Synteny ; Telomere/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Padlock probes: circularizing oligonucleotides for localized DNA detection (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-30
    Description: Nucleotide sequence information derived from DNA segments of the human and other genomes is accumulating rapidly. However, it frequently proves difficult to use such short DNA segments to identify clones in genomic libraries or fragments in blots of the whole genome or for in situ analysis of chromosomes. Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed. Upon recognition of the specific nucleic acid molecule the ends of the probes were joined through the action of a ligase, creating circular DNA molecules catenated to the target sequence. These probes thus provide highly specific detection with minimal background.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nilsson, M -- Malmgren, H -- Samiotaki, M -- Kwiatkowski, M -- Chowdhary, B P -- Landegren, U -- New York, N.Y. -- Science. 1994 Sep 30;265(5181):2085-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beijer Laboratory, Department of Medical Genetics, Biomedical Center, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7522346" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cells, Cultured ; Chromosomes, Human, Pair 12 ; Cystic Fibrosis Transmembrane Conductance Regulator ; DNA/*analysis ; DNA, Circular/*analysis ; Genetic Vectors ; Humans ; In Situ Hybridization ; Lymphocytes ; Membrane Proteins/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Oligonucleotide Probes/chemistry ; Repetitive Sequences, Nucleic Acid ; Templates, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Genome sequence, comparative analysis, and population genetics of the domestic horse (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-11-07
    Description: We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wade, C M -- Giulotto, E -- Sigurdsson, S -- Zoli, M -- Gnerre, S -- Imsland, F -- Lear, T L -- Adelson, D L -- Bailey, E -- Bellone, R R -- Blocker, H -- Distl, O -- Edgar, R C -- Garber, M -- Leeb, T -- Mauceli, E -- MacLeod, J N -- Penedo, M C T -- Raison, J M -- Sharpe, T -- Vogel, J -- Andersson, L -- Antczak, D F -- Biagi, T -- Binns, M M -- Chowdhary, B P -- Coleman, S J -- Della Valle, G -- Fryc, S -- Guerin, G -- Hasegawa, T -- Hill, E W -- Jurka, J -- Kiialainen, A -- Lindgren, G -- Liu, J -- Magnani, E -- Mickelson, J R -- Murray, J -- Nergadze, S G -- Onofrio, R -- Pedroni, S -- Piras, M F -- Raudsepp, T -- Rocchi, M -- Roed, K H -- Ryder, O A -- Searle, S -- Skow, L -- Swinburne, J E -- Syvanen, A C -- Tozaki, T -- Valberg, S J -- Vaudin, M -- White, J R -- Zody, M C -- Broad Institute Genome Sequencing Platform -- Broad Institute Whole Genome Assembly Team -- Lander, E S -- Lindblad-Toh, K -- 098051/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):865-7. doi: 10.1126/science.1178158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. c.wade@usyd.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892987" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/genetics ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Mammalian/*genetics ; Computational Biology ; DNA Copy Number Variations ; Dogs ; Evolution, Molecular ; Female ; Genes ; *Genome ; Haplotypes ; Horses/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
    Electronic Resource
    Electronic Resource
    FISH mapping of seven cDNA sequences in the pig (1997)
    Springer
    Chromosome research 5 (1997), S. 545-549 
    Details
    ISSN: 1573-6849
    Keywords: cDNA ; fluorescence in situhybridization ; pig
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fluorescence in situ hybridization (FISH) technique was applied to localize seven clones derived from a porcine (SSC) intestinal directionally cloned cDNA library. The size of the clones ranged from 1.1 to 1.3 kb. Three of the clones corresponded to histidyl-tRNA synthetase (HARS), immunoglobulin alpha (IGA) and lysozyme (LYZ) and mapped to SSC2q28–q29, 7q2.6 and 5p11 respectively. The available human—pig comparative painting data and sequence homology comparisons assisted in a tentative identification of the other three clones as glutathione-S-transferase (GST), glutathione-S-transferase mu (GSTM1) and immunoglobulin lambda gene cluster (IGL〉1w0,4,14, 5q2.4 and 14q22–q23 respectively. The remaining clone representing an EST mapped to 1p24–p25. These localizations contribute to the transcript map in pig and are significant as comparative markers. Difficulties associated with the mapping of small sequences using FISH are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1018445820059
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  • 5
    Electronic Resource
    Electronic Resource
    Comparative FISH mapping of bovine cosmids to reindeer chromosomes demonstrates conservation of the X-chromosome (1996)
    Springer
    Chromosome research 4 (1996), S. 214-217 
    Details
    ISSN: 1573-6849
    Keywords: cattle ; comparative mapping ; fluorescentin situ hybridization ; reindeer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Three X chromosome-specific bovine cosmids were used for fluorescencein situ hybridization mapping on reindeer (Rangifer tarandus) chromosomes, to test whether such large genomic clones could be used for comparative mapping across distantly related species. All three cosmids showed distinct unique hybridization sites on the reindeer X. Comparative map locations of these cosmids, together with the relative C-banding and genome size data on the X chromosomes of the two species, provide preliminary indications that the short and long arms of bovine X correspond, respectively, to the long and short arms of the reindeer X. The study also demonstrates that cosmid clones can be used successfully for comparative mapping across species that diverged 35 million years ago.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02254962
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  • 6
    Electronic Resource
    Electronic Resource
    Microdissected bovine X chromosome segment delineates homoeologous chromosomal regions in sheep, goat and buffalo (1998)
    Springer
    Chromosome research 6 (1998), S. 213-217 
    Details
    ISSN: 1573-6849
    Keywords: buffalo ; cattle ; chromosome microdissection ; comparative painting ; goat ; sheep
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The terminal part of the long arm of the bovine X chromosome (bands Xq41--q43) was microdissected. The DNA thus obtained was PCR amplified, labelled and used as painting probe on cattle, sheep, goat and buffalo chromosomes. In cattle, as expected, distinct hybridization signals were observed on bands Xq41--q43. In sheep and goat, the painting signals were observed on the proximal part of the long arm of the X chromosome, adjacent to the centromere (Xp12--q12). In buffalo, however, the terminal part of the X chromosome involving bands q44--q47 was painted. The findings contribute towards developing a better understanding of the comparative organization of the X chromosome in the four bovidae species. Proposed models of evolutionary rearrangements within the X chromosome of the four species are examined in light of the results obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009263718667
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  • 7
    Electronic Resource
    Electronic Resource
    Application of three different methods to analyse fibre-FISH results obtained using four lambda clones from the porcine MHC III region (1997)
    Springer
    Chromosome research 5 (1997), S. 247-253 
    Details
    ISSN: 1573-6849
    Keywords: fibre-FISH ; gene mapping ; swine leucocyte antigen (SLA) ; pig
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Four lambda clones (λG11, λC4, λG14 and λ G17) from the porcine MHC class III region were labelled with either biotin-14-dATP or digoxigenin-11-dUTP and hybridized in two different combinations to DNA fibres. The latter were prepared from agarose-embedded porcine peripheral lymphocytes lysed with proteinase K, then spread and fixed on poly-L-lysine-coated slides. Hybridization signals thus obtained confirm the order of the clones previously reported using pulsed-field gel electrophoresis (PFGE). Measurements of probe sizes, gap distances between probes and total length of DNA encompassing the probes were made. Three different methods, namely relative length, Watson—Crick standard and probe size standard-based conversions, were used to estimate the parameters in kilobases. These methods of data conversion were compared with each other and with the available PFGE data, and their utility and accuracy were evaluated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1018419619634
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  • 8
    Electronic Resource
    Electronic Resource
    International system for cytogenetic nomenclature of the domestic horse: Report of the Third International Committee for the Standardization of the Domestic Horse Karyotype, Davis, CA, USA, 1996 (1997)
    Springer
    Chromosome research 5 (1997), S. 433-443 
    Details
    ISSN: 1573-6849
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1018408811881
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  • 9
    Electronic Resource
    Electronic Resource
    Assignment of the linkage group EAM-TYRP2-TPP2 to chromosome 11 in pigs byin situ hybridization mapping of the TPP2 gene (1993)
    Springer
    Chromosome research 1 (1993), S. 175-179 
    Details
    ISSN: 1573-6849
    Keywords: In situ hybridization mapping ; TPP2 ; porcine chromosome II ; Sus scrofa domestica
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms are described for the genes coding for tripeptidyl peptidase II (TPP2) and tyrosinase related protein II (TYRP2) in pigs. A linkage group comprising these loci and the locus for blood group M (EAM) was established by two-point lod score analysis in a three-generation pedigree. Multipoint analysis indicated the linear order EAM-1.1-TYRP2-8.4-TPP2 (recombination distances are given as Kosambi cM). The linkage group was assigned to porcine chromosome 11—the first on this chromosome—throughin situ hybridization mapping of the TPP2 gene. TPP2 is the first gene localized on this chromosome usingin situ hybridization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00710771
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  • 10
    Electronic Resource
    Electronic Resource
    In situ hybridization mapping of the growth hormone receptor (GHR) gene assigns a linkage group (C9, FSA, GHR, and S0105) to Chromosome 16 in pigs (1994)
    Springer
    Mammalian genome 5 (1994), S. 160-162 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00352347
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