A chromosome conformation capture ordered sequence of the barley genome

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we prese...

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Published in:Nature (London) Vol. 544; no. 7651; pp. 427 - 433
Main Authors: Mascher, Martin, Gundlach, Heidrun, Himmelbach, Axel, Beier, Sebastian, Twardziok, Sven O., Wicker, Thomas, Radchuk, Volodymyr, Dockter, Christoph, Hedley, Pete E., Russell, Joanne, Bayer, Micha, Ramsay, Luke, Liu, Hui, Haberer, Georg, Zhang, Xiao-Qi, Zhang, Qisen, Barrero, Roberto A., Li, Lin, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Bolser, Daniel, Colmsee, Christian, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Chailyan, Anna, Sampath, Dharanya, Heavens, Darren, Clissold, Leah, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K., Tan, Cong, Wang, Penghao, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A., Bellgard, Matthew I., Borisjuk, Ljudmilla, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Kersey, Paul, Langridge, Peter, Muehlbauer, Gary J., Clark, Matthew D., Caccamo, Mario, Schulman, Alan H., Mayer, Klaus F. X., Platzer, Matthias, Close, Timothy J., Scholz, Uwe, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Spannagl, Manuel, Li, Chengdao, Waugh, Robbie, Stein, Nils
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 26.04.2017
Nature Publishing Group
Subjects:
631/208/514/1948
631/208/726
631/208/8
631/449/1870
631/449/2491
Agricultural and Veterinary sciences
Agricultural Biotechnology
Artificial chromosomes
Barley
Biologi
Biological Sciences
Bioteknologi med applikationer på växter och djur
Botanik
Botany
Carbohydrates
Cell Nucleus - genetics
Centromere - genetics
Chromatin - genetics
Chromatin - metabolism
Chromosome Mapping
Chromosomes, Artificial, Bacterial - genetics
Chromosomes, Plant - genetics
Cloning
Gene loci
Genetic Variation
Genetics and Breeding in Agricultural Sciences
Genetics and Genomics
Genetik och förädling inom lantbruksvetenskap
Genetik och genomik
Genome, Plant - genetics
Genomes
Genomics
Germplasm
Haplotypes
Haplotypes - genetics
Hordeum - genetics
Humanities and Social Sciences
Lantbruksvetenskap och veterinärmedicin
Meiosis - genetics
multidisciplinary
Natural Sciences
Naturvetenskap
Principal components analysis
Quality
Repetitive Sequences, Nucleic Acid - genetics
Science
Seeds - genetics
ISSN:0028-0836, 1476-4687, 1476-4687
Online Access:Get full text
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Abstract Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley ( Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare . Barley genome sequenced Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley ( Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.
AbstractList Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley ( Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare . Barley genome sequenced Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley ( Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Author Lin, Chongyun
Schulman, Alan H.
Twardziok, Sven O.
Li, Lin
Scholz, Uwe
Clissold, Leah
Wicker, Thomas
Chapman, Brett
Gundlach, Heidrun
Wang, Penghao
Bellgard, Matthew I.
Himmelbach, Axel
Li, Xuan
Kersey, Paul
Ramsay, Luke
Han, Yong
Liu, Hui
Muehlbauer, Gary J.
Zhang, Xiao-Qi
Ounit, Rachid
Muñoz-Amatriaín, María
Caccamo, Mario
Colmsee, Christian
Ayling, Sarah
Šimková, Hana
Chailyan, Anna
Grasso, Stefano
Bolser, Daniel
Felder, Marius
Houben, Andreas
Dai, Fei
Cao, Sujie
Heavens, Darren
McCooke, John K.
Langridge, Peter
Li, Chengdao
Stein, Nils
Haberer, Georg
Hastie, Alex
Zhou, Gaofeng
Russell, Joanne
Wang, Songbo
Poland, Jesse A.
Taudien, Stefan
Tan, Cong
Radchuk, Volodymyr
Platzer, Matthias
Borisjuk, Ljudmilla
Zhang, Guoping
Zhang, Qisen
Li, Hua
Tanskanen, Jaakko
Bayer, Micha
Spannagl, Manuel
Hansson, Mats
Clark, Matthew D.
Mayer, Klaus F. X.
Staňková, Helena
Waugh, Robbie
Aliyeva-Schnorr, Lala
Beier, Sebastian
Schmutzer, Thomas
Vrána, Jan
Chan, Saki
Groth, Marco
Doležel, Jaroslav
Close, Timothy J.
Dockter, Christoph
Wanamaker, Steve
Lonardi, Stefano
Hedley
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/28447635$$D View this record in MEDLINE/PubMed
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Snippet Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized...
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SubjectTerms 631/208/514/1948
631/208/726
631/208/8
631/449/1870
631/449/2491
Agricultural and Veterinary sciences
Agricultural Biotechnology
Artificial chromosomes
Barley
Biologi
Biological Sciences
Bioteknologi med applikationer på växter och djur
Botanik
Botany
Carbohydrates
Cell Nucleus - genetics
Centromere - genetics
Chromatin - genetics
Chromatin - metabolism
Chromosome Mapping
Chromosomes, Artificial, Bacterial - genetics
Chromosomes, Plant - genetics
Cloning
Gene loci
Genetic Variation
Genetics and Breeding in Agricultural Sciences
Genetics and Genomics
Genetik och förädling inom lantbruksvetenskap
Genetik och genomik
Genome, Plant - genetics
Genomes
Genomics
Germplasm
Haplotypes
Haplotypes - genetics
Hordeum - genetics
Humanities and Social Sciences
Lantbruksvetenskap och veterinärmedicin
Meiosis - genetics
multidisciplinary
Natural Sciences
Naturvetenskap
Principal components analysis
Quality
Repetitive Sequences, Nucleic Acid - genetics
Science
Seeds - genetics
Title A chromosome conformation capture ordered sequence of the barley genome
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