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      Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes

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          Abstract

          The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle ( Bos taurus, 2n = 60) and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer ( Rangifer tarandus). We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose ( Alces alces) and are therefore specific to the reindeer.

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          A rapid banding technique for human chromosomes.

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            Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer.

            A version of the polymerase chain reaction (PCR), termed degenerate oligonucleotide-primed PCR (DOP-PCR), which employs oligonucleotides of partially degenerate sequence, has been developed for genome mapping studies. This degeneracy, together with a PCR protocol utilizing a low initial annealing temperature, ensures priming from multiple (e.g., approximately 10(6) in human) evenly dispersed sites within a given genome. Furthermore, as efficient amplification is achieved from the genomes of all species tested using the same primer, the method appears to be species-independent. Thus, for the general amplification of target DNA, DOP-PCR has advantages over interspersed repetitive sequence PCR (IRS-PCR), which relies on the appropriate positioning of species-specific repeat elements. In conjunction with chromosome flow sorting, DOP-PCR has been applied to the characterization of abnormal chromosomes and also to the cloning of new markers for specific chromosome regions. DOP-PCR therefore represents a rapid, efficient, and species-independent technique for general DNA amplification.
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              Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution.

              The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short "hidden" synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: MethodologyRole: Validation
                Role: MethodologyRole: Validation
                Role: Methodology
                Role: Resources
                Role: Funding acquisitionRole: Project administrationRole: Supervision
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 November 2017
                2017
                : 12
                : 11
                : e0187559
                Affiliations
                [1 ] Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
                [2 ] Zoo Prague, Prague, Czech Republic
                University of Florence, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8312-0483
                Article
                PONE-D-17-30791
                10.1371/journal.pone.0187559
                5675437
                29112970
                cbcfbbd1-191d-4835-b6f7-27a4f885fb2f
                © 2017 Frohlich et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 August 2017
                : 21 October 2017
                Page count
                Figures: 7, Tables: 3, Pages: 17
                Funding
                Funded by: CEITEC 2020
                Award ID: LQ1601
                Award Recipient :
                Funded by: Ministry of Agriculture of the Czech Republic
                Award ID: RO 0516
                Award Recipient :
                This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) and by the Ministry of Agriculture of the Czech Republic (RO 0516). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Cloning
                Vector cloning
                BAC cloning
                Research and analysis methods
                Molecular biology techniques
                Cloning
                Vector cloning
                BAC cloning
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomes
                Sex Chromosomes
                X Chromosomes
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bovines
                Cattle
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Ruminants
                Cattle
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Ruminants
                Deer
                Biology and Life Sciences
                Genetics
                Cytogenetics
                Karyotypes
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Hybridization
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Probe Techniques
                Probe Hybridization
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Probe Techniques
                Probe Hybridization
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Gene Mapping
                Chromosome Mapping
                Research and Analysis Methods
                Molecular Biology Techniques
                Gene Mapping
                Chromosome Mapping
                Custom metadata
                All relevant data are within the paper.

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                Uncategorized

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