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Volumn 32, Issue 10, 2014, Pages 1045-1052

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(36)  Li, Ying Hui a   Zhou, Guangyu b,h   Ma, Jianxin c   Jiang, Wenkai b   Jin, Long Guo a   Zhang, Zhouhao b   Guo, Yong a   Zhang, Jinbo b   Sui, Yi a   Zheng, Liangtao b   Zhang, Shan Shan a   Zuo, Qiyang b   Shi, Xue Hui a   Li, Yan Fei a   Zhang, Wan Ke d   Hu, Yiyao b   Kong, Guanyi b   Hong, Hui Long a   Tan, Bing a   Song, Jian a   more..


Author keywords

[No Author keywords available]

Indexed keywords

AGRONOMY; AMINO ACIDS; BIODIVERSITY; CULTIVATION; NITROGEN FIXATION;

EID: 84923019049     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2979     Document Type: Article
Times cited : (503)

References (79)
  • 1
    • 84883252302 scopus 로고    scopus 로고
    • A platform for soybean molecular breeding: The utilization of core collections for food security
    • Qiu, L.J. et al. A platform for soybean molecular breeding: the utilization of core collections for food security. Plant Mol. Biol. 83, 41-50 (2013).
    • (2013) Plant Mol. Biol. , vol.83 , pp. 41-50
    • Qiu, L.J.1
  • 2
    • 74549221016 scopus 로고    scopus 로고
    • Genome sequence of the palaeopolyploid soybean
    • Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183 (2010).
    • (2010) Nature , vol.463 , pp. 178-183
    • Schmutz, J.1
  • 3
    • 78649479141 scopus 로고    scopus 로고
    • Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
    • Lam, H.M. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053-1059 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 1053-1059
    • Lam, H.M.1
  • 4
    • 78650668282 scopus 로고    scopus 로고
    • Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome
    • Kim, M.Y. et al. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl. Acad. Sci. USA 107, 22032-22037 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 22032-22037
    • Kim, M.Y.1
  • 5
    • 84883121798 scopus 로고    scopus 로고
    • Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
    • Li, Y.H. et al. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14, 579 (2013).
    • (2013) BMC Genomics , vol.14 , pp. 579
    • Li, Y.H.1
  • 6
    • 84862993359 scopus 로고    scopus 로고
    • Comparative population genomics of maize domestication and improvement
    • Hufford, M.B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808-811 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 808-811
    • Hufford, M.B.1
  • 7
    • 74049090046 scopus 로고    scopus 로고
    • Building the sequence map of the human pan-genome
    • Li, R. et al. Building the sequence map of the human pan-genome. Nat. Biotechnol. 28, 57-63 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 57-63
    • Li, R.1
  • 8
    • 77956271697 scopus 로고    scopus 로고
    • Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci
    • Li, Y.H. et al. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol. 188, 242-253 (2010).
    • (2010) New Phytol. , vol.188 , pp. 242-253
    • Li, Y.H.1
  • 9
    • 25444524604 scopus 로고    scopus 로고
    • Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial 'pan-genome'
    • Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc. Natl. Acad. Sci. USA 102, 13950-13955 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13950-13955
    • Tettelin, H.1
  • 10
    • 0000878758 scopus 로고
    • Cytological studies on the wild and cultivated Manchurian soybeans
    • Fukuda, Y. Cytological studies on the wild and cultivated Manchurian soybeans. Jap. J. Bot. 6, 489-506 (1933).
    • (1933) Jap. J. Bot. , vol.6 , pp. 489-506
    • Fukuda, Y.1
  • 11
    • 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
  • 12
    • 16644366267 scopus 로고    scopus 로고
    • Plant-specific microtubule-associated protein SPIRAL2 is required for anisotropic growth in Arabidopsis
    • Shoji, T. et al. Plant-specific microtubule-associated protein SPIRAL2 is required for anisotropic growth in Arabidopsis. Plant Physiol. 136, 3933-3944 (2004).
    • (2004) Plant Physiol. , vol.136 , pp. 3933-3944
    • Shoji, T.1
  • 13
    • 79955467963 scopus 로고    scopus 로고
    • Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants
    • Chanda, B. et al. Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants. Nat. Genet. 43, 421-427 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 421-427
    • Chanda, B.1
  • 14
    • 0033823573 scopus 로고    scopus 로고
    • A new subfamily of sucrose transporters, SUT4, with low affinity/high capacity localized in enucleate sieve elements of plants
    • Weise, A. et al. A new subfamily of sucrose transporters, SUT4, with low affinity/high capacity localized in enucleate sieve elements of plants. Plant Cell 12, 1345-1355 (2000).
    • (2000) Plant Cell , vol.12 , pp. 1345-1355
    • Weise, A.1
  • 15
    • 33847365785 scopus 로고    scopus 로고
    • Structural and functional characterization of ferredoxin-ADP+-xidoreductase using knock-out mutants of Arabidopsis
    • Lintala, M. et al. Structural and functional characterization of ferredoxin-ADP+-xidoreductase using knock-out mutants of Arabidopsis. Plant J. 49, 1041-1052 (2007).
    • (2007) Plant J. , vol.49 , pp. 1041-1052
    • Lintala, M.1
  • 16
    • 78549273825 scopus 로고    scopus 로고
    • Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
    • Swanson-Wagner, R.A. et al. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20, 1689-1699 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1689-1699
    • Swanson-Wagner, R.A.1
  • 17
    • 84862981255 scopus 로고    scopus 로고
    • Genome-wide genetic changes during modern breeding of maize
    • Jiao, Y. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812-815 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 812-815
    • Jiao, Y.1
  • 18
    • 79957676298 scopus 로고    scopus 로고
    • Contemporaneous and recent radiations of the world's major succulent plant lineages
    • Arakaki, M. et al. Contemporaneous and recent radiations of the world's major succulent plant lineages. Proc. Natl. Acad. Sci. USA 108, 8379-8384 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 8379-8384
    • Arakaki, M.1
  • 19
    • 84862956715 scopus 로고    scopus 로고
    • Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
    • Varshney, R.K. et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83-89 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 83-89
    • Varshney, R.K.1
  • 20
    • 80455145116 scopus 로고    scopus 로고
    • Archaeological soybean (Glycine max) in East Asia: Does size matter?
    • Lee, G.A., Crawford, G.W., Liu, L., Sasaki, Y. & Chen, X. Archaeological soybean (Glycine max) in East Asia: does size matter? PLoS ONE 6, e26720 (2011).
    • (2011) PLoS ONE , vol.6
    • Lee, G.A.1    Crawford, G.W.2    Liu, L.3    Sasaki, Y.4    Chen, X.5
  • 21
    • 77958580152 scopus 로고    scopus 로고
    • Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
    • Donati, C. et al. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol. 11, R107 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R107
    • Donati, C.1
  • 22
    • 77958497573 scopus 로고    scopus 로고
    • Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes
    • Cai, J.J. & Petrov, D.A. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol. Evol. 2, 393-409 (2010).
    • (2010) Genome Biol. Evol. , vol.2 , pp. 393-409
    • Cai, J.J.1    Petrov, D.A.2
  • 23
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • Krylov, D.M., Wolf, Y.I., Rogozin, I.B. & Koonin, E.V. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13, 2229-2235 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 24
    • 57749105200 scopus 로고    scopus 로고
    • Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean
    • Innes, R.W. et al. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol. 148, 1740-1759 (2008).
    • (2008) Plant Physiol. , vol.148 , pp. 1740-1759
    • Innes, R.W.1
  • 25
    • 84872354931 scopus 로고    scopus 로고
    • The HC-Pro and P3 cistrons of an avirulent soybean mosaic virus are recognized by different resistance genes at the complex Rsv1 locus
    • Wen, R.H., Khatabi, B., Ashfield, T., Maroof, M.S. & Hajimorad, M. The HC-Pro and P3 cistrons of an avirulent soybean mosaic virus are recognized by different resistance genes at the complex Rsv1 locus. Mol. Plant Microbe Interact. 26, 203-215 (2013).
    • (2013) Mol. Plant Microbe Interact. , vol.26 , pp. 203-215
    • Wen, R.H.1    Khatabi, B.2    Ashfield, T.3    Maroof, M.S.4    Hajimorad, M.5
  • 26
    • 78649631946 scopus 로고    scopus 로고
    • SNP assay to detect the 'Hyuuga'red-brown lesion resistance gene for Asian soybean rust
    • Monteros, M.J., Ha, B.-K., Phillips, D.V. & Boerma, H.R. SNP assay to detect the 'Hyuuga'red-brown lesion resistance gene for Asian soybean rust. Theor. Appl. Genet. 121, 1023-1032 (2010).
    • (2010) Theor. Appl. Genet. , vol.121 , pp. 1023-1032
    • Monteros, M.J.1    Ha, B.-K.2    Phillips, D.V.3    Boerma, H.R.4
  • 27
    • 84878348365 scopus 로고    scopus 로고
    • Genetic characterization and fine mapping of the novel Phytophthora resistance gene in a Chinese soybean cultivar
    • Zhang, J. et al. Genetic characterization and fine mapping of the novel Phytophthora resistance gene in a Chinese soybean cultivar. Theor. Appl. Genet. 126, 1555-1561 (2013).
    • (2013) Theor. Appl. Genet. , vol.126 , pp. 1555-1561
    • Zhang, J.1
  • 28
    • 78449297215 scopus 로고    scopus 로고
    • R gene-controlled host specificity in the legume-rhizobia symbiosis
    • Yang, S., Tang, F., Gao, M., Krishnan, H.B. & Zhu, H. R gene-controlled host specificity in the legume-rhizobia symbiosis. Proc. Natl. Acad. Sci. USA 107, 18735-18740 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 18735-18740
    • Yang, S.1    Tang, F.2    Gao, M.3    Krishnan, H.B.4    Zhu, H.5
  • 29
    • 84864692624 scopus 로고    scopus 로고
    • Structural variants in the soybean genome localize to clusters of biotic stress-response genes
    • McHale, L.K. et al. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 159, 1295-1308 (2012).
    • (2012) Plant Physiol. , vol.159 , pp. 1295-1308
    • McHale, L.K.1
  • 30
    • 58149333885 scopus 로고    scopus 로고
    • Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene
    • Liu, B. et al. Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene. Genetics 180, 995-1007 (2008).
    • (2008) Genetics , vol.180 , pp. 995-1007
    • Liu, B.1
  • 31
    • 70350173304 scopus 로고    scopus 로고
    • Map-based cloning of the gene associated with the soybean maturity locus E3
    • Watanabe, S. et al. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics 182, 1251-1262 (2009).
    • (2009) Genetics , vol.182 , pp. 1251-1262
    • Watanabe, S.1
  • 32
    • 78249285587 scopus 로고    scopus 로고
    • Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean
    • Kong, F. et al. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol. 154, 1220-1231 (2010).
    • (2010) Plant Physiol. , vol.154 , pp. 1220-1231
    • Kong, F.1
  • 33
    • 44949165596 scopus 로고    scopus 로고
    • Analysis of quantitative trait loci underlying the period of reproductive growth stages in soybean (Glycine max [L.] Merr.)
    • Xin, D.W. et al. Analysis of quantitative trait loci underlying the period of reproductive growth stages in soybean (Glycine max [L.] Merr.). Euphytica 162, 155-165 (2008).
    • (2008) Euphytica , vol.162 , pp. 155-165
    • Xin, D.W.1
  • 34
    • 84926031098 scopus 로고
    • A study on fat content and fatty acid composition of wild soybean (G. Soja) in China
    • Xu, B. et al. A study on fat content and fatty acid composition of wild soybean (G. soja) in China. Jinlin Agric. Sci. 2, 1-6 (1993).
    • (1993) Jinlin Agric. Sci. , vol.2 , pp. 1-6
    • Xu, B.1
  • 35
    • 78650487543 scopus 로고    scopus 로고
    • Acyl-lipid metabolism
    • Li-Beisson, Y. et al. Acyl-lipid metabolism. The Arabidopsis Book 11, e0161 (2013).
    • (2013) The Arabidopsis Book , vol.11 , pp. e0161
    • Li-Beisson, Y.1
  • 36
    • 70350234774 scopus 로고    scopus 로고
    • Fatty acid-derived signals in plant defense
    • Kachroo, A. & Kachroo, P. Fatty acid-derived signals in plant defense. Annu. Rev. Phytopathol. 47, 153-176 (2009).
    • (2009) Annu. Rev. Phytopathol. , vol.47 , pp. 153-176
    • Kachroo, A.1    Kachroo, P.2
  • 37
    • 27944511234 scopus 로고    scopus 로고
    • Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY1 complex in plant innate immunity
    • Feys, B.J. et al. Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY1 complex in plant innate immunity. Plant Cell 17, 2601-2613 (2005).
    • (2005) Plant Cell , vol.17 , pp. 2601-2613
    • Feys, B.J.1
  • 38
    • 79955687733 scopus 로고    scopus 로고
    • Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes
    • Qi, Z.M. et al. Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica 179, 499-514 (2011).
    • (2011) Euphytica , vol.179 , pp. 499-514
    • Qi, Z.M.1
  • 39
    • 79958055201 scopus 로고    scopus 로고
    • ABI4 activates DGAT1 expression in Arabidopsis seedlings during nitrogen deficiency
    • Yang, Y., Yu, X., Song, L. & An, C. ABI4 activates DGAT1 expression in Arabidopsis seedlings during nitrogen deficiency. Plant Physiol. 156, 873-883 (2011).
    • (2011) Plant Physiol. , vol.156 , pp. 873-883
    • Yang, Y.1    Yu, X.2    Song, L.3    An, C.4
  • 40
    • 84881613734 scopus 로고    scopus 로고
    • Using the candidate gene approach for detecting genes underlying seed oil concentration and yield in soybean
    • Eskandari, M., Cober, E.R. & Rajcan, I. Using the candidate gene approach for detecting genes underlying seed oil concentration and yield in soybean. Theor. Appl. Genet. 126, 1839-1850 (2013).
    • (2013) Theor. Appl. Genet. , vol.126 , pp. 1839-1850
    • Eskandari, M.1    Cober, E.R.2    Rajcan, I.3
  • 41
    • 1542321063 scopus 로고    scopus 로고
    • Identification of putative QTL that underlie yield in interspecific soybean backcross populations
    • Wang, D., Graef, G., Procopiuk, A. & Diers, B. Identification of putative QTL that underlie yield in interspecific soybean backcross populations. Theor. Appl. Genet. 108, 458-467 (2004).
    • (2004) Theor. Appl. Genet. , vol.108 , pp. 458-467
    • Wang, D.1    Graef, G.2    Procopiuk, A.3    Diers, B.4
  • 42
    • 23044455690 scopus 로고    scopus 로고
    • Cytokinin oxidase regulates rice grain production
    • Ashikari, M. et al. Cytokinin oxidase regulates rice grain production. Science 309, 741-745 (2005).
    • (2005) Science , vol.309 , pp. 741-745
    • Ashikari, M.1
  • 43
    • 79959832855 scopus 로고    scopus 로고
    • Genetic control of plant organ growth
    • Johnson, K. & Lenhard, M. Genetic control of plant organ growth. New Phytol. 191, 319-333 (2011).
    • (2011) New Phytol. , vol.191 , pp. 319-333
    • Johnson, K.1    Lenhard, M.2
  • 44
    • 84880840905 scopus 로고    scopus 로고
    • Why assembling plant genome sequences is so challenging
    • Claros, M.G. et al. Why assembling plant genome sequences is so challenging. Biology 1, 439-459 (2012).
    • (2012) Biology , vol.1 , pp. 439-459
    • Claros, M.G.1
  • 46
    • 84880511242 scopus 로고    scopus 로고
    • Pan genome of the phytoplankton Emiliania underpins its global distribution
    • Read, B.A. et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-213 (2013).
    • (2013) Nature , vol.499 , pp. 209-213
    • Read, B.A.1
  • 47
    • 84896808010 scopus 로고    scopus 로고
    • Insights into the maize pan-genome and pan-transcriptome
    • Hirsch, C.N. et al. Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26, 121-135 (2014).
    • (2014) Plant Cell , vol.26 , pp. 121-135
    • Hirsch, C.N.1
  • 48
    • 33750964714 scopus 로고    scopus 로고
    • Impacts of genetic bottlenecks on soybean genome diversity
    • Hyten, D.L. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103, 16666-16671 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 16666-16671
    • Hyten, D.L.1
  • 49
    • 33845618112 scopus 로고    scopus 로고
    • The molecular genetics of crop domestication
    • Doebley, J.F., Gaut, B.S. & Smith, B.D. The molecular genetics of crop domestication. Cell 127, 1309-1321 (2006).
    • (2006) Cell , vol.127 , pp. 1309-1321
    • Doebley, J.F.1    Gaut, B.S.2    Smith, B.D.3
  • 50
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of Drosophila
    • Myers, E.W. et al. A whole-genome assembly of Drosophila. Science 287, 2196-2204 (2000).
    • (2000) Science , vol.287 , pp. 2196-2204
    • Myers, E.W.1
  • 52
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Butler, J. et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810-820 (2008).
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1
  • 53
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
    • (2004) Genome Biol. , vol.5 , pp. R12
    • Kurtz, S.1
  • 54
    • 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
  • 55
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 56
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215-ii225 (2003).
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 59
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1
  • 60
    • 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
  • 61
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    • Haas, B.J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R7
    • Haas, B.J.1
  • 62
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Punta, M. et al. The Pfam protein families database. Nucleic Acids Res. 40, D290-D301 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. D290-D301
    • Punta, M.1
  • 63
    • 23144458473 scopus 로고    scopus 로고
    • InterProScan: Protein domains identifier
    • Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. W116-W120
    • Quevillon, E.1
  • 64
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: Tool for the unification of biology
    • Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29 (2000).
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 65
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 66
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C.J. & 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
  • 67
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 68
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F. & Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197 (1981).
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 69
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
    • Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 70
    • 33847173733 scopus 로고    scopus 로고
    • FUNC: A package for detecting significant associations between gene sets and ontological annotations
    • Prüfer, K. et al. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8, 41 (2007).
    • (2007) BMC Bioinformatics , vol.8 , pp. 41
    • Prüfer, K.1
  • 72
    • 77649149766 scopus 로고    scopus 로고
    • SoyTEdb: A comprehensive database of transposable elements in the soybean genome
    • Du, J. et al. SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11, 113 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 113
    • Du, J.1
  • 73
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 74
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 75
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556 (1997).
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 76
    • 79551599525 scopus 로고    scopus 로고
    • Mugsy: Fast multiple alignment of closely related whole genomes
    • Angiuoli, S.V. & Salzberg, S.L. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27, 334-342 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 334-342
    • Angiuoli, S.V.1    Salzberg, S.L.2
  • 77
    • 84864701726 scopus 로고    scopus 로고
    • Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean
    • Kang, Y. et al. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol. 12, 139 (2012).
    • (2012) BMC Plant Biol. , vol.12 , pp. 139
    • Kang, Y.1
  • 78
    • 82255181391 scopus 로고    scopus 로고
    • RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and-susceptible alleles
    • Kim, K.H. et al. RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and-susceptible alleles. DNA Res. 18, 483-497 (2011).
    • (2011) DNA Res. , vol.18 , pp. 483-497
    • Kim, K.H.1
  • 79
    • 84867981440 scopus 로고    scopus 로고
    • The Rsv3 locus conferring resistance to soybean mosaic virus is associated with a cluster of coiled-coil nucleotide-binding leucine-rich repeat genes
    • Suh, S.J. et al. The Rsv3 locus conferring resistance to soybean mosaic virus is associated with a cluster of coiled-coil nucleotide-binding leucine-rich repeat genes. Plant Genome 4, 55-64 (2011).
    • (2011) Plant Genome , vol.4 , pp. 55-64
    • Suh, S.J.1


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