A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes
Publication Date
December 29, 2006
Journal
PLOS Genetics
Authors
Lucia Carbone, Gery M Vessere, Boudewijn F.H. Ten Hallers, Baoli Zhu, et al
Volume
2
Issue
12
Pages
e223
DOI
http://doi.org/10.1371/journal.pgen.0020223
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.0020223
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17196042
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1756914
Europe PMC
http://europepmc.org/abstract/MED/17196042
Web of Science
000243482100019
Scopus
33846908783
Mendeley
http://www.mendeley.com/research/highresolution-map-synteny-disruptions-gibbon-human-genomes
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/469725", "https://ndownloader.figshare.com/files/469837", "https://ndownloader.figshare.com/files/469846", "https://ndownloader.figshare.com/files/469851", "https://ndownloader.figshare.com/files/469865", "https://ndownloader.figshare.com/files/469874"], "description"=>"<div><p>Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) <em>(Nomascus leucogenys leucogenys)</em> as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon–human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state.</p></div>", "links"=>[], "tags"=>["high-resolution", "synteny", "disruptions", "gibbon", "genomes"], "article_id"=>152592, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0020223.sg001", "https://dx.doi.org/10.1371/journal.pgen.0020223.sg002", "https://dx.doi.org/10.1371/journal.pgen.0020223.sg003", "https://dx.doi.org/10.1371/journal.pgen.0020223.sd001", "https://dx.doi.org/10.1371/journal.pgen.0020223.st001", "https://dx.doi.org/10.1371/journal.pgen.0020223.st002"], "stats"=>{"downloads"=>22, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_High_Resolution_Map_of_Synteny_Disruptions_in_Gibbon_and_Human_Genomes/152592", "title"=>"A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-12-29 00:43:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/954216"], "description"=>"<div><p>(A) The figure shows the sampling distribution of the overlap between SDs and a random set of regions obtained by relocating our original sample 1,000 times in the corresponding chromosomes. The original sample fell more than three standard deviations away from the mean of the simulated distribution (red arrow).</p><p>(B) The regions from the original sample were expanded in 100 kb increments. The number of regions overlapping with SDs at each step is shown.</p><p>(C) We measured the amount of overlap (in base pairs) of our 100 regions, while shifting each of them up to 5 Mb left and right of their original positions in 100 kb increments. The strong correlation between the original position (red arrow) and SD content is shown.</p></div>", "links"=>[], "tags"=>["breakpoint", "regions", "segmental"], "article_id"=>624499, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020223.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_of_the_Breakpoint_Regions_with_Segmental_Duplication_/624499", "title"=>"Association of the Breakpoint Regions with Segmental Duplication", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/953918"], "description"=>"<p>Ideogram of human chromosomes with orthologous gibbon chromosomes identified by array painting represented by colored bars to the left of each chromosome. Each segment is named after the gibbon chromosome followed by a small letter that refers to its mapping order in the gibbon chromosome. The BOSRs have been defined for convenience by numbers (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020223#pgen-0020223-t001\" target=\"_blank\">Table 1</a>). Gibbon clones spanning breakpoints identified by BES mapping are also located on the map. Clones with map positions that disagree with the array-painting map are italicized.</p>", "links"=>[], "tags"=>["gibbon"], "article_id"=>624212, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020223.g002", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_Map_of_Human_and_Gibbon_Chromosomes_/624212", "title"=>"Comparative Map of Human and Gibbon Chromosomes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:55:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/954083"], "description"=>"<div><p>(A) FISH experiments to validate breakpoints identified by array painting. Images 1 and 2 show hybridization on NLE metaphase preparations with human BACs spanning breakpoints identified by array painting. The yellow color in image 1 is due to the overlap of red and green spots as both BACs map on the same chromosome. Image 3 shows a similar experiment done on HLA metaphase preparations. The reciprocal position of the BACs used in each experiment is shown in the boxes below the images.</p><p>(B) FISH validation experiments on six gibbon BAC clones spanning three reciprocal breakpoints for the same rearrangement. In the diagrams, the rearrangements are illustrated starting from the ancestral chromosome form. Abbreviation: AC, ancestral chromosome.</p><p>(C) Gibbon BACs spanning inversion breakpoints were tested by FISH on human and gibbon metaphases. A BAC spanning an inversion in gibbon is expected to give a split signal on the human chromosome and a single signal on the corresponding gibbon chromosome.</p></div>", "links"=>[], "tags"=>["validation"], "article_id"=>624374, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020223.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Breakpoint_Validation_by_FISH_/624374", "title"=>"Breakpoint Validation by FISH", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:56:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/954340"], "description"=>"<p>Two sequenced gibbon clones spanning rearrangement breakpoints revealed the presence of additional segments of synteny not observed by other methods. In both cases, the first break of synteny was found to contain SDs and the second to contain interspersed repeats.</p>", "links"=>[], "tags"=>["sequenced", "gibbon", "bac"], "article_id"=>624622, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020223.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Fully_Sequenced_Gibbon_BAC_Clones_/624622", "title"=>"Analysis of Fully Sequenced Gibbon BAC Clones", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:58:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/953801"], "description"=>"<div><p>(A and B) The plotted value of Log<sub>2</sub> ratio/chromosome length for human Chromosome 2 after hybridization with sorted gibbon chromosomes NLE14 and NLE19, respectively.</p><p>(C) Results of the application of the difference method to the datasets in (A) and (B). After canceling out the systematic variation, it is possible to discern three different regions from left to right, one amplified (1), one deleted (2), and one at the baseline (3).</p></div>", "links"=>[], "tags"=>["synteny", "regions"], "article_id"=>624095, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Lucia Carbone", "Gery M Vessere", "Boudewijn F.H. ten Hallers", "Baoli Zhu", "Kazutoyo Osoegawa", "Alan Mootnick", "Andrea Kofler", "Johannes Wienberg", "Jane Rogers", "Sean Humphray", "Carol Scott", "R. Alan Harris", "Aleksandar Milosavljevic", "Pieter J de Jong"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020223.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_Break_of_Synteny_Regions_Using_the_Log_2_Ratio_Difference_Method_/624095", "title"=>"Identification of Break of Synteny Regions Using the Log<sub>2</sub> Ratio Difference Method", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:54:25"}

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  • {"unique-ip"=>"4", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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Relative Metric

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