A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence

Larkin, Denis M.; Wind, Annelie Everts-van der; Rebeiz, Mark; Schweitzer, Peter A.; Bachman, Sharon L.; Green, Cheryl; Wright, Chris; Campos, Edhilvia J.; Benson, Leslie D.; Edwards, Jennifer; Liu, Lei; Osoegawa, Kazutoyo; Womack, James E.; Jong, Pieter J. de; Lewin, Harris A.

doi:10.1101/gr.1560203

Cited by 124 publications

(4 citation statements)

References 24 publications

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“…It results in the lower bound bound(e) = 4 [37] that also gives a good approximation for br(e). On the other hand, one can estimate br(e 1 , e 2 ) as the number bound(e 1 , e 2 ) of vertices shared between non-trivial cycles in the breakpoint graphs corresponding to the branches e 1 and e 2 (similar approach was used in [22] and later explored in [25,31]). Assuming that the genomes at the internal nodes of the phylogenetic tree can be reliably reconstructed [4,25,26,45], one can compute bound(e) and bound(e 1 , e 2 ) for all (pairs of) branches.…”

Section: Inter-and Intra-breakpoint Reusementioning

confidence: 99%

Limited Lifespan of Fragile Regions in Mammalian Evolution

Alekseyev

Pevzner

2010

Comparative Genomics

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An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

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Section: Inter-and Intra-breakpoint Reusementioning

confidence: 99%

Limited Lifespan of Fragile Regions in Mammalian Evolution

Alekseyev

Pevzner

2010

Comparative Genomics

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“…-genetic maps (14,16,18,61,85,86,105,131) -physical maps (14,16,18,74,107,137) -EST collections (14,16,18,20,102,103,105,125) -SNP collections (14,49,125) -large-insert (e.g. BAC) libraries (16,18,73,96,105).…”

Section: Farm Animal Resourcesmentioning

confidence: 99%

“…Gene indices have also been constructed or are under construction for various species (14,102,105,113,114,115). Comparative maps were developed concurrently with genetic maps and are continuously being refined to link farm animal genome information with the more advanced structural and functional genomic data of other species, such as humans and mice (14,16,18,29,64,73,78,105). Recently developed comparative mapping tools (47,64,78)…”

Section: Farm Animal Resourcesmentioning

confidence: 99%

La genómica funcional: herramientas para mejorar la sanidad y el bienestar del ganado

Hiendleder¹,

BAUERSACHS²,

Boulesteix³

et al. 2005

Rev. Sci. Tech. OIE

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The first genome sequence assemblies of farm animal species are now accessible through public domain databases, and further sequencing projects are in rapid progress. In addition, large collections of expressed sequences have been obtained, which will aid in constructing annotated transcript maps for many economically important species. Thus, the breeding of farm animals is entering the post-genome era. Functional genomics, defined as applying global experimental approaches to assess gene function, by using the information and reagents provided by structural genomics (i.e. mapping and sequencing), has become the focus of interest. Combining a holistic view of phenotypes at the molecular level with genetic marker data seems a particularly promising approach for improving health and welfare traits in farm animals. These traits are often difficult to define. They suffer from low heritabilities and a corresponding lack of genetic gain in conventional selection and breeding programmes. At the same time, genomic information from micro-organisms and parasites offers the potential for new vaccines and therapeutics. This review describes major functional genomics tools, lists genomic resources available for farm animals and discusses the prospects and challenges of functional genomics in improving the health and welfare of farm animals.

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“…The locations of microsatellites were analyzed using a new version of COMPASS software (with the kind help of Dr. Harris A. Lewin, University of Illinois at Urbana-Champaing, IL, USA) to predict the position of each microsatellite on Hanwoo chromosomes (Larkin et al, 2003).…”

Section: Pcr Primer Design and Chromosome Localizationmentioning

confidence: 99%

Identification of New Microsatellite DNAs in the Chromosomal DNA of the Korean Cattle (Hanwoo)

Kim¹,

Hong²,

Lee³

et al. 2004

Asian Australas. J. Anim. Sci

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To isolate the microsatellites from the chromosomal DNA of the Korean cattle (Hanwoo) and to use those for the genetic selection, four bacteriophage genomic libraries containing the chromosomal DNA of six Hanwoo steers showing the differences in meat quality and quantity were used. Screening of the genomic libraries using 32 P-radiolabeled 5`-(CA) 12 -3' nucleotide as a probe, resulted in isolation of about 3,000 positive candidate bacteriophage clones that contain (CA) n -type dinucleotide microsatellites. After confirming the presence of microsatellite in each positive candidate clone by Southern blot analysis, the DNA fragments that include microsatellite and flanking sequences possessing less than 2 kb in size, were subcloned into plasmid vector. Results from the analysis of microsatellite length polymorphism, using twenty-two PCR primers designed from flanking region of each microsatellite DNA, demonstrated that 208 and 210 alleles of HW-YU-MS#3 were closely related to the economic traits such as marbling score, daily gain, backfat thickness and M. longissimus dorsi area in Hanwoo. Interestingly, HW-YU-MS#3 microsatellite was localized in bovine chromosome 17 on which QTLs related to regulation of the body fat content and muscle hypertrophy locus are previously known to exist. Taken together, the results from the present study suggest the possible use of the two alleles as a DNA marker related to economic trait to select the Hanwoo in the future.

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A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence

Cited by 124 publications

References 24 publications

Limited Lifespan of Fragile Regions in Mammalian Evolution

Limited Lifespan of Fragile Regions in Mammalian Evolution

La genómica funcional: herramientas para mejorar la sanidad y el bienestar del ganado

Identification of New Microsatellite DNAs in the Chromosomal DNA of the Korean Cattle (Hanwoo)

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