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Volumn 544, Issue 7651, 2017, Pages 427-433

A chromosome conformation capture ordered sequence of the barley genome

(76)  Mascher, Martin a,b   Gundlach, Heidrun c   Himmelbach, Axel a   Beier, Sebastian a   Twardziok, Sven O c   Wicker, Thomas d   Radchuk, Volodymyr a   Dockter, Christoph e   Hedley, Pete E f   Russell, Joanne f   Bayer, Micha f   Ramsay, Luke f   Liu, Hui f   Haberer, Georg c   Zhang, Xiao Qi g   Zhang, Qisen h   Barrero, Roberto A g   Li, Lin i   Taudien, Stefan j   Groth, Marco j   more..


Author keywords

[No Author keywords available]

Indexed keywords

BARLEY; BREEDING; CARBOHYDRATE; CHROMOSOME; GENE; GENETIC ANALYSIS; GENOME; GERMPLASM; GRASS; RECOMBINATION; TEMPERATE ENVIRONMENT;

EID: 85018282934     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature22043     Document Type: Article
Times cited : (1092)

References (99)
  • 1
    • 0000358478 scopus 로고
    • Archaeological studies in the Levant 1. Neolithic sites in the Damascus basin: Aswad, Ghoraifé, Ramad
    • van Zeist, W., Bakker-Heeres, J. A. H. Archaeological studies in the Levant 1. Neolithic sites in the Damascus basin: Aswad, Ghoraifé, Ramad. Palaeohistoria 24, 165-256 (1985).
    • (1985) Palaeohistoria , vol.24 , pp. 165-256
    • Van Zeist, W.1    Bakker-Heeres, J.A.H.2
  • 2
    • 84879749302 scopus 로고    scopus 로고
    • Emergence of agriculture in the foothills of the Zagros Mountains of Iran
    • Riehl, S., Zeidi, M., Conard, N. J. Emergence of agriculture in the foothills of the Zagros Mountains of Iran. Science 341, 65-67 (2013).
    • (2013) Science , vol.341 , pp. 65-67
    • Riehl, S.1    Zeidi, M.2    Conard, N.J.3
  • 3
    • 84865975468 scopus 로고    scopus 로고
    • The role of cult and feasting in the emergence of Neolithic communities. New evidence from Göbekli Tepe, south-eastern Turkey
    • Dietrich, O., Heun, M., Notroff, J., Schmidt, K., Zarnkow, M. The role of cult and feasting in the emergence of Neolithic communities. New evidence from Göbekli Tepe, south-eastern Turkey. Antiquity 86, 674-695 (2012).
    • (2012) Antiquity , vol.86 , pp. 674-695
    • Dietrich, O.1    Heun, M.2    Notroff, J.3    Schmidt, K.4    Zarnkow, M.5
  • 4
    • 84873526598 scopus 로고    scopus 로고
    • What was brewing in the Natufian? An archaeological assessment of brewing technology in the Epipaleolithic
    • Hayden, B., Canuel, N., Shanse, J. What was brewing in the Natufian? An archaeological assessment of brewing technology in the Epipaleolithic. J. Archaeol. Method Theory 20, 102-150 (2013).
    • (2013) J. Archaeol. Method Theory , vol.20 , pp. 102-150
    • Hayden, B.1    Canuel, N.2    Shanse, J.3
  • 5
    • 84973375251 scopus 로고    scopus 로고
    • Revealing a 5, 000-y-old beer recipe in China
    • Wang, J., et al. Revealing a 5, 000-y-old beer recipe in China. Proc. Natl Acad. Sci. USA 113, 6444-6448 (2016).
    • (2016) Proc. Natl Acad. Sci. USA , vol.113 , pp. 6444-6448
    • Wang, J.1
  • 7
    • 84870265846 scopus 로고    scopus 로고
    • A physical, genetic and functional sequence assembly of the barley genome
    • International Barley Genome Sequencing Consortium.
    • International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature 491, 711-716 (2012).
    • (2012) Nature , vol.491 , pp. 711-716
  • 8
    • 84893818298 scopus 로고    scopus 로고
    • PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses
    • Yang, P., et al. PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc. Natl Acad. Sci. USA 111, 2104-2109 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 2104-2109
    • Yang, P.1
  • 9
    • 84938409570 scopus 로고    scopus 로고
    • Evolution of the grain dispersal system in barley
    • Pourkheirandish, M., et al. Evolution of the grain dispersal system in barley. Cell 162, 527-539 (2015).
    • (2015) Cell , vol.162 , pp. 527-539
    • Pourkheirandish, M.1
  • 10
    • 84978742666 scopus 로고    scopus 로고
    • Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation
    • Russell, J., et al. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat. Genet. 48, 1024-1030 (2016).
    • (2016) Nat. Genet. , vol.48 , pp. 1024-1030
    • Russell, J.1
  • 11
    • 0343986281 scopus 로고    scopus 로고
    • Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints
    • Künzel, G., Korzun, L., Meister, A. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154, 397-412 (2000).
    • (2000) Genetics , vol.154 , pp. 397-412
    • Künzel, G.1    Korzun, L.2    Meister, A.3
  • 12
    • 85028275552 scopus 로고    scopus 로고
    • Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes
    • Beier, S., et al. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. Plant Biotechnol. J. 14, 1511-1522 (2016).
    • (2016) Plant Biotechnol. J. , vol.14 , pp. 1511-1522
    • Beier, S.1
  • 13
    • 84942794562 scopus 로고    scopus 로고
    • Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome
    • Munoz-Amatriaín, M., et al. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J. 84, 216-227 (2015).
    • (2015) Plant J. , vol.84 , pp. 216-227
    • Munoz-Amatriaín, M.1
  • 14
    • 84929174408 scopus 로고    scopus 로고
    • CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
    • Ounit, R., Wanamaker, S., Close, T. J., Lonardi, S. CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16, 236 (2015).
    • (2015) BMC Genomics , vol.16 , pp. 236
    • Ounit, R.1    Wanamaker, S.2    Close, T.J.3    Lonardi, S.4
  • 15
    • 84930929520 scopus 로고    scopus 로고
    • BARLEX-the barley draft genome explorer
    • Colmsee, C., et al. BARLEX-the Barley Draft Genome Explorer. Mol. Plant 8, 964-966 (2015).
    • (2015) Mol. Plant , vol.8 , pp. 964-966
    • Colmsee, C.1
  • 16
    • 84891808629 scopus 로고    scopus 로고
    • A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms
    • Ariyadasa, R., et al. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant Physiol. 164, 412-423 (2014).
    • (2014) Plant Physiol. , vol.164 , pp. 412-423
    • Ariyadasa, R.1
  • 17
    • 84886793453 scopus 로고    scopus 로고
    • Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
    • Mascher, M., et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76, 718-727 (2013).
    • (2013) Plant J. , vol.76 , pp. 718-727
    • Mascher, M.1
  • 18
    • 84864883566 scopus 로고    scopus 로고
    • Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
    • Lam, E. T., et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771-776 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 771-776
    • Lam, E.T.1
  • 19
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and populationbased modeling
    • Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., Chen, L. Genome architectures revealed by tethered chromosome conformation capture and populationbased modeling. Nat. Biotechnol. 30, 90-98 (2011).
    • (2011) Nat. Biotechnol. , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5
  • 20
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 21
    • 84890034912 scopus 로고    scopus 로고
    • Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
    • Burton, J. N., et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1119-1125
    • Burton, J.N.1
  • 22
    • 85018297524 scopus 로고    scopus 로고
    • Construction of a map-based reference genome sequence for barley Hordeum vulgare L
    • Beier, S., et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci. Data 4, 170044 (2017).
    • (2017) Sci. Data , vol.4 , pp. 170044
    • Beier, S.1
  • 23
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
    • Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., Zdobnov, E. M. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 3210-3212
    • Simao, F.A.1    Waterhouse, R.M.2    Ioannidis, P.3    Kriventseva, E.V.4    Zdobnov, E.M.5
  • 24
    • 0030049360 scopus 로고    scopus 로고
    • Chromosome 'painting' plants-A feasible technique?
    • Fuchs, J., Houben, A., Brandes, A., Schubert, I. Chromosome 'painting' in plants-A feasible technique? Chromosoma 104, 315-320 (1996).
    • (1996) Chromosoma , vol.104 , pp. 315-320
    • Fuchs, J.1    Houben, A.2    Brandes, A.3    Schubert, I.4
  • 25
    • 84921643810 scopus 로고    scopus 로고
    • Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila
    • Grob, S., Schmid, M. W., Grossniklaus, U. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila. Mol. Cell 55, 678-693 (2014).
    • (2014) Mol. Cell , vol.55 , pp. 678-693
    • Grob, S.1    Schmid, M.W.2    Grossniklaus, U.3
  • 26
    • 77952744854 scopus 로고    scopus 로고
    • A three-dimensional model of the yeast genome
    • Duan, Z., et al. A three-dimensional model of the yeast genome. Nature 465, 363-367 (2010).
    • (2010) Nature , vol.465 , pp. 363-367
    • Duan, Z.1
  • 27
    • 84855278504 scopus 로고    scopus 로고
    • Chromosome organization and dynamics during interphase, mitosis, meiosis in plants
    • Tiang, C. L., He, Y., Pawlowski, W. P. Chromosome organization and dynamics during interphase, mitosis, meiosis in plants. Plant Physiol. 158, 26-34 (2012).
    • (2012) Plant Physiol. , vol.158 , pp. 26-34
    • Tiang, C.L.1    He, Y.2    Pawlowski, W.P.3
  • 28
    • 84919949716 scopus 로고    scopus 로고
    • A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
    • Rao, S. S., et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
    • (2014) Cell , vol.159 , pp. 1665-1680
    • Rao, S.S.1
  • 29
    • 0037356770 scopus 로고    scopus 로고
    • Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content
    • Houben, A., et al. Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. 33, 967-973 (2003).
    • (2003) Plant J. , vol.33 , pp. 967-973
    • Houben, A.1
  • 30
    • 0016351896 scopus 로고
    • Genome size and the proportion of repeated nucleotide sequence DNA in plants
    • Flavell, R. B., Bennett, M. D., Smith, J. B., Smith, D. B. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12, 257-269 (1974).
    • (1974) Biochem. Genet. , vol.12 , pp. 257-269
    • Flavell, R.B.1    Bennett, M.D.2    Smith, J.B.3    Smith, D.B.4
  • 31
    • 0013630297 scopus 로고    scopus 로고
    • Nested retrotransposons in the intergenic regions of the maize genome
    • SanMiguel, P., et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768 (1996).
    • (1996) Science , vol.274 , pp. 765-768
    • SanMiguel, P.1
  • 32
    • 0037700013 scopus 로고    scopus 로고
    • TREP: A database for Triticeae repetitive elements
    • Wicker, T., Matthews, D. E., Keller, B. TREP: A database for Triticeae repetitive elements. Trends Plant Sci. 7, 561-562 (2002).
    • (2002) Trends Plant Sci. , vol.7 , pp. 561-562
    • Wicker, T.1    Matthews, D.E.2    Keller, B.3
  • 33
    • 84904390032 scopus 로고    scopus 로고
    • Structural and functional partitioning of bread wheat chromosome 3B
    • Choulet, F., et al. Structural and functional partitioning of bread wheat chromosome 3B. Science 345, 1249721 (2014).
    • (2014) Science , vol.345 , pp. 1249721
    • Choulet, F.1
  • 34
    • 0028450046 scopus 로고
    • Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants
    • Bureau, T. E., Wessler, S. R. Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6, 907-916 (1994).
    • (1994) Plant Cell , vol.6 , pp. 907-916
    • Bureau, T.E.1    Wessler, S.R.2
  • 35
    • 0028053180 scopus 로고
    • Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses
    • Bureau, T. E., Wessler, S. R. Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc. Natl Acad. Sci. USA 91, 1411-1415 (1994).
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 1411-1415
    • Bureau, T.E.1    Wessler, S.R.2
  • 36
    • 0033057257 scopus 로고    scopus 로고
    • Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons
    • Malik, H. S., Eickbush, T. H. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol. 73, 5186-5190 (1999).
    • (1999) J. Virol. , vol.73 , pp. 5186-5190
    • Malik, H.S.1    Eickbush, T.H.2
  • 37
    • 0346801873 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • Harris, M. A., et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. D258-D261
    • Harris, M.A.1
  • 38
    • 0025429268 scopus 로고
    • Classification and characterization of the rice ?-amylase multigene family
    • Huang, N., Sutliff, T. D., Litts, J. C., Rodriguez, R. L. Classification and characterization of the rice ?-amylase multigene family. Plant Mol. Biol. 14, 655-668 (1990).
    • (1990) Plant Mol. Biol. , vol.14 , pp. 655-668
    • Huang, N.1    Sutliff, T.D.2    Litts, J.C.3    Rodriguez, R.L.4
  • 39
    • 0021771014 scopus 로고
    • Structural genes for ?-amylases are located on barley chromosomes 1 and 6
    • Muthukrishnan, S., Gill, B. S., Swegle, M., Chandra, G. R. Structural genes for ?-amylases are located on barley chromosomes 1 and 6. J. Biol. Chem. 259, 13637-13639 (1984).
    • (1984) J. Biol. Chem. , vol.259 , pp. 13637-13639
    • Muthukrishnan, S.1    Gill, B.S.2    Swegle, M.3    Chandra, G.R.4
  • 40
    • 0024289516 scopus 로고
    • Barley ?-amylase genes. Quantitative comparison of steady-state mRNA levels from individual members of the two different families expressed in aleurone cells
    • Khursheed, B., Rogers, J. C. Barley ?-amylase genes. Quantitative comparison of steady-state mRNA levels from individual members of the two different families expressed in aleurone cells. J. Biol. Chem. 263, 18953-18960 (1988).
    • (1988) J. Biol. Chem. , vol.263 , pp. 18953-18960
    • Khursheed, B.1    Rogers, J.C.2
  • 41
    • 80053207269 scopus 로고    scopus 로고
    • Dynamic 13C/1H NMR imaging uncovers sugar allocation in the living seed
    • Melkus, G., et al. Dynamic 13C/1H NMR imaging uncovers sugar allocation in the living seed. Plant Biotechnol. J. 9, 1022-1037 (2011).
    • (2011) Plant Biotechnol. J. , vol.9 , pp. 1022-1037
    • Melkus, G.1
  • 42
    • 84855846270 scopus 로고    scopus 로고
    • Sucrose efflux mediated by SWEET proteins as a key step for phloem transport
    • Chen, L. Q., et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science 335, 207-211 (2012).
    • (2012) Science , vol.335 , pp. 207-211
    • Chen, L.Q.1
  • 43
    • 84907835067 scopus 로고    scopus 로고
    • Caspase-like activities accompany programmed cell death events in developing barley grains
    • Tran, V., Weier, D., Radchuk, R., Thiel, J., Radchuk, V. Caspase-like activities accompany programmed cell death events in developing barley grains. PLoS ONE 9, e109426 (2014).
    • (2014) PLoS ONE , vol.9 , pp. e109426
    • Tran, V.1    Weier, D.2    Radchuk, R.3    Thiel, J.4    Radchuk, V.5
  • 44
    • 84870541655 scopus 로고    scopus 로고
    • Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley
    • Comadran, J., et al. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat. Genet. 44, 1388-1392 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 1388-1392
    • Comadran, J.1
  • 45
    • 58549119732 scopus 로고    scopus 로고
    • Identification and verification of QTLs for agronomic traits using wild barley introgression lines
    • Schmalenbach, I., León, J., Pillen, K. Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor. Appl. Genet. 118, 483-497 (2009).
    • (2009) Theor. Appl. Genet. , vol.118 , pp. 483-497
    • Schmalenbach, I.1    León, J.2    Pillen, K.3
  • 46
    • 34248995357 scopus 로고    scopus 로고
    • Dissection of a malting quality QTL region on chromosome 1 (7H) of barley
    • Han, F., et al. Dissection of a malting quality QTL region on chromosome 1 (7H) of barley. Mol. Breed. 14, 339-347 (2004).
    • (2004) Mol. Breed. , vol.14 , pp. 339-347
    • Han, F.1
  • 47
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, dynamics
    • Schnable, P. S., et al. The B73 maize genome: Complexity, diversity, dynamics. Science 326, 1112-1115 (2009).
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1
  • 49
    • 84938423867 scopus 로고    scopus 로고
    • Assembly and diploid architecture of an individual human genome via single-molecule technologies
    • Pendleton, M., et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780-786 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 780-786
    • Pendleton, M.1
  • 50
    • 85006263051 scopus 로고    scopus 로고
    • Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
    • Hirsch, C., et al. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell 28, 2700-2714 (2016).
    • (2016) Plant Cell , vol.28 , pp. 2700-2714
    • Hirsch, C.1
  • 52
    • 71549121654 scopus 로고    scopus 로고
    • De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
    • Steuernagel, B., et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 10, 547 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 547
    • Steuernagel, B.1
  • 53
    • 80053981849 scopus 로고    scopus 로고
    • Sequencing of BAC pools by different next generation sequencing platforms and strategies
    • Taudien, S., et al. Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res. Notes 4, 411 (2011).
    • (2011) BMC Res. Notes , vol.4 , pp. 411
    • Taudien, S.1
  • 54
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R., et al. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 55
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J. T., et al. ABySS: A parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 56
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 58
    • 84870379849 scopus 로고    scopus 로고
    • Hi-C: A comprehensive technique to capture the conformation of genomes
    • Belton, J. M., et al. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods 58, 268-276 (2012).
    • (2012) Methods , vol.58 , pp. 268-276
    • Belton, J.M.1
  • 59
    • 84975475885 scopus 로고    scopus 로고
    • BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
    • Stan? ková, H., et al. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol. J. 14, 1523-1531 (2016).
    • (2016) Plant Biotechnol. J. , vol.14 , pp. 1523-1531
    • Stanková, H.1
  • 60
    • 0032734071 scopus 로고    scopus 로고
    • Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L. )
    • Lysák, M. A., et al. Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L. ). Chromosome Res. 7, 431-444 (1999).
    • (1999) Chromosome Res. , vol.7 , pp. 431-444
    • Lysák, M.A.1
  • 61
    • 0012828041 scopus 로고    scopus 로고
    • Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips
    • Šimková, H., C? íhalíková, J., Vrána, J., Lysák, M., Doležel, J. Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol. Plant. 46, 369-373 (2003).
    • (2003) Biol. Plant. , vol.46 , pp. 369-373
    • Šimková, H.1    Cíhalíková, J.2    Vrána, J.3    Lysák, M.4    Doležel, J.5
  • 62
    • 84923794054 scopus 로고    scopus 로고
    • Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
    • Cao, H., et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience 3, 34 (2014).
    • (2014) Gigascience , vol.3 , pp. 34
    • Cao, H.1
  • 64
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi, G., Nepusz, T. The igraph software package for complex network research. InterJournal Complex Syst. 1695 (2006).
    • (2006) Inter Journal Complex Syst. , vol.1695
    • Csardi, G.1    Nepusz, T.2
  • 65
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10-12 (2011).
    • (2011) EMBnet. J. , vol.17 , pp. 10-12
    • Martin, M.1
  • 67
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R., Hall, I. M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 68
    • 84870463249 scopus 로고    scopus 로고
    • HiCNorm: Removing biases in Hi-C data via Poisson regression
    • Hu, M., et al. HiCNorm: Removing biases in Hi-C data via Poisson regression. Bioinformatics 28, 3131-3133 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 3131-3133
    • Hu, M.1
  • 70
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 71
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • DePristo, M.A.1
  • 72
    • 84943626821 scopus 로고    scopus 로고
    • Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H
    • Aliyeva-Schnorr, L., et al. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J. 84, 385-394 (2015).
    • (2015) Plant J. , vol.84 , pp. 385-394
    • Aliyeva-Schnorr, L.1
  • 73
    • 0035945274 scopus 로고    scopus 로고
    • Sequence organization of barley centromeres
    • Hudakova, S., et al. Sequence organization of barley centromeres. Nucleic Acids Res. 29, 5029-5035 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 5029-5035
    • Hudakova, S.1
  • 74
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project.
    • International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793-800 (2005).
    • (2005) Nature , vol.436 , pp. 793-800
  • 75
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative.
    • International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768 (2010).
    • (2010) Nature , vol.463 , pp. 763-768
  • 76
    • 58449137410 scopus 로고    scopus 로고
    • The Sorghum bicolor genome and the diversification of grasses
    • Paterson, A. H., et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556 (2009).
    • (2009) Nature , vol.457 , pp. 551-556
    • Paterson, A.H.1
  • 77
    • 79956012836 scopus 로고    scopus 로고
    • Comprehensive sequence analysis of 24, 783 barley full-length cDNAs derived from 12 clone libraries
    • Matsumoto, T., et al. Comprehensive sequence analysis of 24, 783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 156, 20-28 (2011).
    • (2011) Plant Physiol. , vol.156 , pp. 20-28
    • Matsumoto, T.1
  • 78
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 80
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative.
    • Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815 (2000).
    • (2000) Nature , vol.408 , pp. 796-815
  • 81
    • 84979609001 scopus 로고    scopus 로고
    • PGSB PlantsDB: Updates to the database framework for comparative plant genome research
    • Spannagl, M., et al. PGSB PlantsDB: Updates to the database framework for comparative plant genome research. Nucleic Acids Res. 44 (D1), D1141-D1147 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D1141-D1147
    • Spannagl, M.1
  • 82
    • 39749179047 scopus 로고    scopus 로고
    • LTRharvest an efficient and flexible software for de novo detection of LTR retrotransposons
    • Ellinghaus, D., Kurtz, S., Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9, 18 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 18
    • Ellinghaus, D.1    Kurtz, S.2    Willhoeft, U.3
  • 83
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy, S. R. Accelerated profile HMM searches. PLOS Comput. Biol. 7, e1002195 (2011).
    • (2011) PLOS Comput. Biol. , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 85
    • 84887962140 scopus 로고    scopus 로고
    • GenomeTools: A comprehensive software library for efficient processing of structured genome annotations
    • Gremme, G., Steinbiss, S., Kurtz, S. GenomeTools: A comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans. Comput. Biol. Bioinformatics 10, 645-656 (2013).
    • (2013) IEEE/ACM Trans. Comput. Biol. Bioinformatics , vol.10 , pp. 645-656
    • Gremme, G.1    Steinbiss, S.2    Kurtz, S.3
  • 86
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman, A., et al. The Pfam protein families database. Nucleic Acids Res. 32, D138-D141 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. D138-D141
    • Bateman, A.1
  • 87
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen, T. N., Brunak, S., von Heijne, G., Nielsen, H. SignalP 4. 0: Discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 88
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas, A., Van Dyke, M., Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162-1164 (1991).
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 89
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. Jr, Roos, D. S. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 90
    • 84946074228 scopus 로고    scopus 로고
    • Ensembl Plants: Integrating tools for visualizing, mining, analyzing plant genomics data
    • Bolser, D., Staines, D. M., Pritchard, E., Kersey, P. Ensembl Plants: Integrating tools for visualizing, mining, analyzing plant genomics data. Methods Mol. Biol. 1374, 115-140 (2016).
    • (2016) Methods Mol. Biol. , vol.1374 , pp. 115-140
    • Bolser, D.1    Staines, D.M.2    Pritchard, E.3    Kersey, P.4
  • 91
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R. C., et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
    • (2004) Genome Biol. , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 92
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of Gene Ontology terms
    • Supek, F., Bošnjak, M., Škunca, N., Šmuc, T. REVIGO summarizes and visualizes long lists of Gene Ontology terms. PLoS ONE 6, e21800 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e21800
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 93
    • 79251510532 scopus 로고    scopus 로고
    • Development of maternal seed tissue in barley is mediated by regulated cell expansion and cell disintegration and coordinated with endosperm growth
    • Radchuk, V., Weier, D., Radchuk, R., Weschke, W., Weber, H. Development of maternal seed tissue in barley is mediated by regulated cell expansion and cell disintegration and coordinated with endosperm growth. J. Exp. Bot. 62, 1217-1227 (2011).
    • (2011) J. Exp. Bot. , vol.62 , pp. 1217-1227
    • Radchuk, V.1    Weier, D.2    Radchuk, R.3    Weschke, W.4    Weber, H.5
  • 94
    • 84885672827 scopus 로고    scopus 로고
    • Barley whole exome capture: A tool for genomic research in the genus Hordeum and beyond
    • Mascher, M., et al. Barley whole exome capture: A tool for genomic research in the genus Hordeum and beyond. Plant J. 76, 494-505 (2013).
    • (2013) Plant J. , vol.76 , pp. 494-505
    • Mascher, M.1
  • 95
    • 77949512406 scopus 로고    scopus 로고
    • Tablet-next generation sequence assembly visualization
    • Milne, I., et al. Tablet-next generation sequence assembly visualization. Bioinformatics 26, 401-402 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 401-402
    • Milne, I.1
  • 96
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: Analysis and visualization of LD and haplotype maps
    • Barrett, J. C., Fry, B., Maller, J., Daly, M. J. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4
  • 97
    • 79951776750 scopus 로고    scopus 로고
    • Flapjack-graphical genotype visualization
    • Milne, I., et al. Flapjack-graphical genotype visualization. Bioinformatics 26, 3133-3134 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 3133-3134
    • Milne, I.1
  • 98
    • 84867293252 scopus 로고    scopus 로고
    • GenAlEx 6. 5: Genetic analysis in Excel. Population genetic software for teaching and research-an update
    • Peakall, R., Smouse, P. E. GenAlEx 6. 5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 2537-2539
    • Peakall, R.1    Smouse, P.E.2
  • 99
    • 84904382612 scopus 로고    scopus 로고
    • A chromosomebased draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
    • The International Wheat Genome Sequencing Consortium.
    • The International Wheat Genome Sequencing Consortium. A chromosomebased draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).
    • (2014) Science , vol.345 , pp. 1251788


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