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Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species
A. Himmelbach, A. Ruban, I. Walde, H. Šimková, J. Doležel, A. Hastie, N. Stein, M. Mascher,
Language English Country England, Great Britain
Document type Journal Article, Research Support, Non-U.S. Gov't
NLK
Free Medical Journals
from 1991 to 1 year ago
Wiley Free Content
from 1997 to 1 year ago
PubMed
30256471
DOI
10.1111/tpj.14109
Knihovny.cz E-resources
- MeSH
- Chromosome Inversion genetics MeSH
- Chromosomes, Plant genetics MeSH
- Genome, Plant genetics MeSH
- Genotype MeSH
- In Situ Hybridization, Fluorescence MeSH
- Hordeum genetics MeSH
- Chromosome Mapping MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor-intensive and lack sensitivity. Here, we report the use of three-dimensional contact probabilities between genomic loci as assayed by chromosome-conformation capture sequencing (Hi-C) to detect multi-megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi-C as a generally applicable method for inversion discovery in natural populations.
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- $a Himmelbach, Axel $u Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
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- $a Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species / $c A. Himmelbach, A. Ruban, I. Walde, H. Šimková, J. Doležel, A. Hastie, N. Stein, M. Mascher,
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- $a Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor-intensive and lack sensitivity. Here, we report the use of three-dimensional contact probabilities between genomic loci as assayed by chromosome-conformation capture sequencing (Hi-C) to detect multi-megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi-C as a generally applicable method for inversion discovery in natural populations.
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- $a Ruban, Alevtina $u Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
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- $a Walde, Ines $u Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
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- $a Šimková, Hana $u Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
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- $a Doležel, Jaroslav $u Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
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- $a Hastie, Alex $u BioNano Genomics Inc., 9640 Towne Centre Drive, San Diego, CA, 92121, USA.
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- $a Mascher, Martin $u Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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- $w MED00003838 $t The Plant journal : for cell and molecular biology $x 1365-313X $g Roč. 96, č. 6 (2018), s. 1309-1316
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