메뉴 건너뛰기




Volumn 4, Issue , 2014, Pages

Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGY; FEMALE; GENE LIBRARY; GENETIC POLYMORPHISM; GENETICS; GENOME; GENOMICS; GENOTYPE; HAPLOIDY; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; PROCEDURES; PUFFER FISH; REPRODUCIBILITY;

EID: 84925477292     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06780     Document Type: Article
Times cited : (22)

References (31)
  • 1
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and de novo assembly of the giant panda genome
    • Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
    • (2010) Nature , vol.463 , pp. 311-317
    • Li, R.1
  • 2
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • The Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195 (2011).
    • (2011) Nature , vol.475 , pp. 189-195
  • 3
    • 80052606169 scopus 로고    scopus 로고
    • The genome sequence of Atlantic cod reveals a unique immune system
    • Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207-210 (2011).
    • (2011) Nature , vol.477 , pp. 207-210
    • Star, B.1
  • 4
    • 84859700415 scopus 로고    scopus 로고
    • Draft genome of the pearl oyster Pinctada fucata: A platform for understanding bivalve biology
    • Takeuchi, T. et al. Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res 19, 117-130 (2012).
    • (2012) DNA Res , vol.19 , pp. 117-130
    • Takeuchi, T.1
  • 5
    • 84867088834 scopus 로고    scopus 로고
    • The oyster genome reveals stress adaptation and complexity of shell formation
    • Zhang, G. et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490, 49-54 (2012).
    • (2012) Nature , vol.490 , pp. 49-54
    • Zhang, G.1
  • 6
    • 84878420758 scopus 로고    scopus 로고
    • The Norway spruce genome sequence and conifer genome evolution
    • Nystedt, B. et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497, 579-584 (2013).
    • (2013) Nature , vol.497 , pp. 579-584
    • Nystedt, B.1
  • 7
    • 84873087245 scopus 로고    scopus 로고
    • A heterozygous moth genome provides insights into herbivory and detoxification
    • You, M. et al. A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet 45, 220-225 (2013).
    • (2013) Nat Genet , vol.45 , pp. 220-225
    • You, M.1
  • 8
    • 84889261375 scopus 로고    scopus 로고
    • High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus
    • Zheng, W. et al. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. Nat Commun 4, 2673 (2013).
    • (2013) Nat Commun , vol.4 , pp. 2673
    • Zheng, W.1
  • 9
    • 84903203459 scopus 로고    scopus 로고
    • The genome of Eucalyptus grandis
    • Myburg, A. et al. The genome of Eucalyptus grandis. Nature 510, 356-362 (2014).
    • (2014) Nature , vol.510 , pp. 356-362
    • Myburg, A.1
  • 10
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan, C., Sajjadian, S. & Eichler, E. E. Limitations of next-generation genome sequence assembly. Nat Methods 8, 61-65 (2011).
    • (2011) Nat Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 11
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre, S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108, 1513-1518 (2011).
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 1513-1518
    • Gnerre, S.1
  • 12
    • 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
  • 13
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20, 265-272 (2010).
    • (2010) Genome Res , vol.20 , pp. 265-272
    • Li, R.1
  • 14
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821-829 (2008).
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 15
    • 84905667070 scopus 로고    scopus 로고
    • Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
    • Kajitani, R. et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24, 1384-95 (2014).
    • (2014) Genome Res , vol.24 , pp. 1384-1395
    • Kajitani, R.1
  • 16
    • 0037162885 scopus 로고    scopus 로고
    • Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    • Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310 (2002).
    • (2002) Science , vol.297 , pp. 1301-1310
    • Aparicio, S.1
  • 17
    • 79960102692 scopus 로고    scopus 로고
    • Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals
    • Kai, W. et al. Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol 3, 424-442 (2011).
    • (2011) Genome Biol Evol , vol.3 , pp. 424-442
    • Kai, W.1
  • 18
    • 84872119842 scopus 로고    scopus 로고
    • Assessment of homozygosity levels in the mito-gynogenetic torafugu (Takifugu rubripes) by genome-wide SNP analyses
    • Zhang, H. et al. Assessment of homozygosity levels in the mito-gynogenetic torafugu (Takifugu rubripes) by genome-wide SNP analyses. Aquaculture 380, 114-119 (2013).
    • (2013) Aquaculture , vol.380 , pp. 114-119
    • Zhang, H.1
  • 19
    • 0347375427 scopus 로고
    • Artificial gynogenesis and its application in genetic and selective breeding of fishes
    • Blaxter, J.H.S. Ed. Springer Verlag, Berlin
    • Stanley, J. G. & Snne, K. E. Artificial gynogenesis and its application in genetic and selective breeding of fishes. In The Early Life History of Fish, Blaxter, J.H.S. Ed. Springer Verlag, Berlin 526 (1974)
    • (1974) The Early Life History of Fish , vol.526
    • Stanley, J.G.1    Snne, K.E.2
  • 20
    • 0001334245 scopus 로고
    • Artificial androgenesis induced with gemma irradiation in masu salmon, Oncorhynchus masou
    • Arai, K., Onozato, H. & Yamazaki, F. Artificial androgenesis induced with gemma irradiation in masu salmon, Oncorhynchus masou. Bull. Fac. Fish Hokkaido Univ. 30, 181 (1979)
    • (1979) Bull. Fac. Fish Hokkaido Univ. , vol.30 , pp. 181
    • Arai, K.1    Onozato, H.2    Yamazaki, F.3
  • 21
    • 0019452034 scopus 로고
    • Production of clones of homozygous diploid zebra fish (Brachydanio rerio)
    • Streisinger, G., Walker, C., Dower, N., Knauber, D. & Singer, F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293-296 (1981).
    • (1981) Nature , vol.291 , pp. 293-296
    • Streisinger, G.1    Walker, C.2    Dower, N.3    Knauber, D.4    Singer, F.5
  • 22
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R. K. T. 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.K.T.1
  • 23
    • 83055181941 scopus 로고    scopus 로고
    • Assemblathon 1: A competitive assessment of de novo short read assembly methods
    • Earl, D. et al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Res 21, 2224-2241 (2011).
    • (2011) Genome Res , vol.21 , pp. 2224-2241
    • Earl, D.1
  • 24
    • 84857893016 scopus 로고    scopus 로고
    • GAGE: A critical evaluation of genome assemblies and assembly algorithms
    • Salzberg, S. L. et al. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res 22, 557-567 (2012).
    • (2012) Genome Res , vol.22 , pp. 557-567
    • Salzberg, S.L.1
  • 25
    • 79960655760 scopus 로고    scopus 로고
    • The DNA sequence of human chromosome 22
    • Dunham, I. et al. The DNA sequence of human chromosome 22. Nature 402, 489-495 (1999).
    • (1999) Nature , vol.402 , pp. 489-495
    • Dunham, I.1
  • 26
    • 3242808027 scopus 로고    scopus 로고
    • Large-scale copy number polymorphism in the human genome
    • Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004).
    • (2004) Science , vol.305 , pp. 525-528
    • Sebat, J.1
  • 27
    • 77949831756 scopus 로고    scopus 로고
    • Structural variation in the human genome and its role in disease
    • Stankiewicz, P. & Lupski, J. R. Structural Variation in the Human Genome and its Role in Disease. Annu Rev Med 61, 437-455 (2010).
    • (2010) Annu Rev Med , vol.61 , pp. 437-455
    • Stankiewicz, P.1    Lupski, J.R.2
  • 28
    • 84862491113 scopus 로고    scopus 로고
    • Mechanisms for recurrent and complex human genomic rearrangements
    • Liu, P., Carvalho, C. M. B., Hastings, P. J. & Lupski, J. R. Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22, 211-220 (2012).
    • (2012) Curr Opin Genet Dev , vol.22 , pp. 211-220
    • Liu, P.1    Carvalho, C.M.B.2    Hastings, P.J.3    Lupski, J.R.4
  • 29
    • 25444457773 scopus 로고    scopus 로고
    • Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    • Taudien, S. et al. Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence. BMC Genom 5 (2004).
    • (2004) BMC Genom , vol.5
    • Taudien, S.1
  • 30
    • 71049176982 scopus 로고    scopus 로고
    • Genome 10k: A proposal to obtain whole-genome sequence for 10 000 vertebrate species
    • Haussler, D. et al. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. Journal of Heredity 100, 659-674 (2009).
    • (2009) Journal of Heredity , vol.100 , pp. 659-674
    • Haussler, D.1
  • 31
    • 84865192446 scopus 로고    scopus 로고
    • The fishes of Genome 10K
    • Bernardi, G. et al. The fishes of Genome 10K. Mar Genom 7, 3-6 (2012).
    • (2012) Mar Genom , vol.7 , pp. 3-6
    • Bernardi, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.