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Volumn 9, Issue 1, 2018, Pages

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia

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MALTOSE;

EID: 85050020985     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-018-05106-7     Document Type: Article
Times cited : (182)

References (76)
  • 1
    • 19944403184 scopus 로고    scopus 로고
    • Fermented beverages of pre-and proto-historic China
    • McGovern, P. E. et al. Fermented beverages of pre-and proto-historic China. Proc. Natl Acad. Sci. USA 101, 17593-17598 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17593-17598
    • McGovern, P.E.1
  • 2
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau, A. et al. Life with 6000 genes. Science 274, 563-547 (1996).
    • (1996) Science , vol.274 , pp. 547-563
    • Goffeau, A.1
  • 4
    • 84899638426 scopus 로고    scopus 로고
    • Current perspectives and the future of domestication studies
    • Larson, G. et al. Current perspectives and the future of domestication studies. Proc. Natl. Acad. Sci. USA 111, 6139-6146 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 6139-6146
    • Larson, G.1
  • 5
    • 85014003757 scopus 로고    scopus 로고
    • The fascinating and secret wild life of the budding yeast S
    • Liti, G. The fascinating and secret wild life of the budding yeast S. cerevisiae. eLife 4, e05835 (2015).
    • (2015) Cerevisiae. ELife , vol.4 , pp. e05835
    • Liti, G.1
  • 6
    • 33645096818 scopus 로고    scopus 로고
    • Evidence for domesticated and wild populations of Saccharomyces cerevisiae
    • Fay, J. C. &Benavides, J. A. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS. Genet. 1, 66-71 (2005).
    • (2005) PLoS. Genet. , vol.1 , pp. 66-71
    • Fay, J.C.1    Benavides, J.A.2
  • 7
    • 0036224204 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics
    • Sniegowski, P. D., Dombrowski, P. G. &Fingerman, E. Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res. 1, 299-306 (2002).
    • (2002) FEMS Yeast Res. , vol.1 , pp. 299-306
    • Sniegowski, P.D.1    Dombrowski, P.G.2    Fingerman, E.3
  • 8
    • 84962191016 scopus 로고    scopus 로고
    • Independent origins of yeast associated with coffee and cacao fermentation
    • Ludlow, C. L. et al. Independent origins of yeast associated with coffee and cacao fermentation. Curr. Biol. 26, 965-971 (2016).
    • (2016) Curr. Biol. , vol.26 , pp. 965-971
    • Ludlow, C.L.1
  • 10
    • 70349515584 scopus 로고    scopus 로고
    • Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118
    • Novo, M. et al. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc. Natl Acad. Sci. USA 106, 16333-16338 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 16333-16338
    • Novo, M.1
  • 11
    • 77649242421 scopus 로고    scopus 로고
    • Evidence for widespread adaptive evolution of gene expression in budding yeast
    • Fraser, H. B., Moses, A. M. &Schadt, E. E. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc. Natl Acad. Sci. USA 107, 2977-2982 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 2977-2982
    • Fraser, H.B.1    Moses, A.M.2    Schadt, E.E.3
  • 12
    • 79952420028 scopus 로고    scopus 로고
    • Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex
    • Sicard, D. &Legras, J. L. Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C. R. Biol. 334, 229-236 (2011).
    • (2011) C. R. Biol. , vol.334 , pp. 229-236
    • Sicard, D.1    Legras, J.L.2
  • 13
    • 79952262678 scopus 로고    scopus 로고
    • Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae
    • Borneman, A. R. et al. Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet. 7, e1001287 (2011).
    • (2011) PLoS Genet. , vol.7 , pp. e1001287
    • Borneman, A.R.1
  • 14
    • 84925847939 scopus 로고    scopus 로고
    • Genomic insights into the Saccharomyces sensu stricto complex
    • Borneman, A. R. &Pretorius, I. S. Genomic insights into the Saccharomyces sensu stricto complex. Genetics 199, 281-291 (2015).
    • (2015) Genetics , vol.199 , pp. 281-291
    • Borneman, A.R.1    Pretorius, I.S.2
  • 15
    • 84936861677 scopus 로고    scopus 로고
    • Evolutionary advantage conferred by an eukaryote-toeukaryote gene transfer event in wine yeasts
    • Marsit, S. et al. Evolutionary advantage conferred by an eukaryote-toeukaryote gene transfer event in wine yeasts. Mol. Biol. Evol. 32, 1695-1707 (2015).
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 1695-1707
    • Marsit, S.1
  • 16
    • 85018194017 scopus 로고    scopus 로고
    • Diversity and adaptive evolution of Saccharomyces wine yeast: A review
    • Marsit, S. &Dequin, S. Diversity and adaptive evolution of Saccharomyces wine yeast: a review. FEMS Yeast Res. 15, fov067 (2015).
    • (2015) FEMS Yeast Res. , vol.15 , pp. fov067
    • Marsit, S.1    Dequin, S.2
  • 18
    • 84986322634 scopus 로고    scopus 로고
    • Domestication and divergence of Saccharomyces cerevisiae beer yeasts
    • e1316
    • Gallone, B. et al. Domestication and divergence of Saccharomyces cerevisiae beer yeasts. Cell 166, 1397-1410 e1316 (2016).
    • (2016) Cell , vol.166 , pp. 1397-1410
    • Gallone, B.1
  • 19
    • 84992021857 scopus 로고    scopus 로고
    • Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts
    • Goncalves, M. et al. Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr. Biol. 26, 2750-2761 (2016).
    • (2016) Curr. Biol. , vol.26 , pp. 2750-2761
    • Goncalves, M.1
  • 20
    • 62649089109 scopus 로고    scopus 로고
    • Population genomics of domestic and wild yeasts
    • Liti, G. et al. Population genomics of domestic and wild yeasts. Nature 458, 337-341 (2009).
    • (2009) Nature , vol.458 , pp. 337-341
    • Liti, G.1
  • 21
    • 73349121287 scopus 로고    scopus 로고
    • A distinct population of Saccharomyces cerevisiae in New Zealand: Evidence for local dispersal by insects and human-aided global dispersal in oak barrels
    • Goddard, M. R., Anfang, N., Tang, R., Gardner, R. C. &Jun, C. A distinct population of Saccharomyces cerevisiae in New Zealand: evidence for local dispersal by insects and human-aided global dispersal in oak barrels. Environ. Microbiol. 12, 63-73 (2010).
    • (2010) Environ. Microbiol. , vol.12 , pp. 63-73
    • Goddard, M.R.1    Anfang, N.2    Tang, R.3    Gardner, R.C.4    Jun, C.5
  • 22
    • 79959847334 scopus 로고    scopus 로고
    • Trait variation in yeast is defined by population history
    • Warringer, J. et al. Trait variation in yeast is defined by population history. PLoS Genet. 7, e1002111 (2011).
    • (2011) PLoS Genet. , vol.7 , pp. e1002111
    • Warringer, J.1
  • 23
    • 84863587188 scopus 로고    scopus 로고
    • Life history shapes trait heredity by accumulation of loss-offunction alleles in yeast
    • Zörgö, E. et al. Life history shapes trait heredity by accumulation of loss-offunction alleles in yeast. Mol. Biol. Evol. 29, 1781-1789 (2012).
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1781-1789
    • Zörgö, E.1
  • 24
    • 34248192358 scopus 로고    scopus 로고
    • Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history
    • Legras, J. L., Merdinoglu, D., Cornuet, J. M. &Karst, F. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16, 2091-2102 (2007).
    • (2007) Mol. Ecol. , vol.16 , pp. 2091-2102
    • Legras, J.L.1    Merdinoglu, D.2    Cornuet, J.M.3    Karst, F.4
  • 25
    • 62649126517 scopus 로고    scopus 로고
    • Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
    • Schacherer, J., Shapiro, J. A., Ruderfer, D. M. &Kruglyak, L. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458, 342-345 (2009).
    • (2009) Nature , vol.458 , pp. 342-345
    • Schacherer, J.1    Shapiro, J.A.2    Ruderfer, D.M.3    Kruglyak, L.4
  • 26
    • 84890831000 scopus 로고    scopus 로고
    • Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq
    • Cromie, G. A. et al. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3, 2163-2171 (2013).
    • (2013) G3 (Bethesda) , vol.3 , pp. 2163-2171
    • Cromie, G.A.1
  • 27
    • 84945452256 scopus 로고    scopus 로고
    • A population genomics insight into the Mediterranean origins of wine yeast domestication
    • Almeida, P. et al. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol. Ecol. 24, 5412-5427 (2015).
    • (2015) Mol. Ecol. , vol.24 , pp. 5412-5427
    • Almeida, P.1
  • 28
    • 84868206362 scopus 로고    scopus 로고
    • Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity
    • Wang, Q. M., Liu, W. Q., Liti, G., Wang, S. A. &Bai, F. Y. Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol. Ecol. 21, 5404-5417 (2012).
    • (2012) Mol. Ecol. , vol.21 , pp. 5404-5417
    • Wang, Q.M.1    Liu, W.Q.2    Liti, G.3    Wang, S.A.4    Bai, F.Y.5
  • 29
    • 0002370878 scopus 로고
    • The East Asia is a probable land of the cultured yeasts Saccharomyces cerevisiae (in Russia)
    • Naumov, G. I. &Nikonenko, P. E. The East Asia is a probable land of the cultured yeasts Saccharomyces cerevisiae (in Russia). Izv. Sib. Otd. Akad. Nauk SSSR Seriya Biol. Nauk 20, 97-101 (1988).
    • (1988) Izv. Sib. Otd. Akad. Nauk SSSR Seriya Biol. Nauk , vol.20 , pp. 97-101
    • Naumov, G.I.1    Nikonenko, P.E.2
  • 30
    • 3543032259 scopus 로고    scopus 로고
    • The finding of the yeast species Saccharomyces bayanus in Far East Asia
    • Naumov, G. I., Gazdiev, D. O. &Naumova, E. S. The finding of the yeast species Saccharomyces bayanus in Far East Asia. Microbiology 72, 738-743 (2003).
    • (2003) Microbiology , vol.72 , pp. 738-743
    • Naumov, G.I.1    Gazdiev, D.O.2    Naumova, E.S.3
  • 31
    • 84901060647 scopus 로고    scopus 로고
    • Evidence for a Far East Asian origin of lager beer yeast
    • Bing, J., Han, P. J., Liu, W. Q., Wang, Q. M. &Bai, F. Y. Evidence for a Far East Asian origin of lager beer yeast. Curr. Biol. 24, R380-R381 (2014).
    • (2014) Curr. Biol. , vol.24 , pp. R380-R381
    • Bing, J.1    Han, P.J.2    Liu, W.Q.3    Wang, Q.M.4    Bai, F.Y.5
  • 32
    • 84953410740 scopus 로고    scopus 로고
    • Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests
    • Gayevskiy, V. &Goddard, M. R. Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests. Environ. Microbiol. 18, 1137-1147 (2016).
    • (2016) Environ. Microbiol. , vol.18 , pp. 1137-1147
    • Gayevskiy, V.1    Goddard, M.R.2
  • 33
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • Alexander, D. H., Novembre, J. &Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 34
    • 79952129813 scopus 로고    scopus 로고
    • Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae
    • Magwene, P. M. et al. Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 108, 1987-1992 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 1987-1992
    • Magwene, P.M.1
  • 35
    • 4344689976 scopus 로고    scopus 로고
    • Arsenical resistance genes in Saccharomyces douglasii and other yeast species undergo rapid evolution involving genomic rearrangements and duplications
    • Maciaszczyk, E., Wysocki, R., Golik, P., Lazowska, J. &Ulaszewski, S. Arsenical resistance genes in Saccharomyces douglasii and other yeast species undergo rapid evolution involving genomic rearrangements and duplications. FEMS Yeast Res. 4, 821-832 (2004).
    • (2004) FEMS Yeast Res. , vol.4 , pp. 821-832
    • Maciaszczyk, E.1    Wysocki, R.2    Golik, P.3    Lazowska, J.4    Ulaszewski, S.5
  • 36
    • 84897883016 scopus 로고    scopus 로고
    • A high-definition view of functional genetic variation from natural yeast genomes
    • Bergstrom, A. et al. A high-definition view of functional genetic variation from natural yeast genomes. Mol. Biol. Evol. 31, 872-888 (2014).
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 872-888
    • Bergstrom, A.1
  • 37
    • 73249135142 scopus 로고    scopus 로고
    • Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production
    • Argueso, J. L. et al. Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res. 19, 2258-2270 (2009).
    • (2009) Genome Res. , vol.19 , pp. 2258-2270
    • Argueso, J.L.1
  • 38
    • 42049085470 scopus 로고    scopus 로고
    • Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S
    • Sampaio, J. P. &Goncalves, P. Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Appl. Environ. Microbiol. 74, 2144-2152 (2008).
    • (2008) Cerevisiae and S. Paradoxus. Appl. Environ. Microbiol. , vol.74 , pp. 2144-2152
    • Sampaio, J.P.1    Goncalves, P.2
  • 39
    • 85007240758 scopus 로고    scopus 로고
    • Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae
    • Barbosa, R. et al. Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae. Genome Biol. Evol. 8, 317-329 (2016).
    • (2016) Genome Biol. Evol. , vol.8 , pp. 317-329
    • Barbosa, R.1
  • 40
    • 84921544218 scopus 로고    scopus 로고
    • Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation
    • Knight, S. &Goddard, M. R. Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation. ISME J. 9, 361-370 (2015).
    • (2015) ISME J. , vol.9 , pp. 361-370
    • Knight, S.1    Goddard, M.R.2
  • 41
    • 84937231900 scopus 로고    scopus 로고
    • Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages
    • Tapsoba, F., Legras, J. L., Savadogo, A., Dequin, S. &Traore, A. S. Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages. Int. J. Food Microbiol. 211, 128-133 (2015).
    • (2015) Int. J. Food Microbiol. , vol.211 , pp. 128-133
    • Tapsoba, F.1    Legras, J.L.2    Savadogo, A.3    Dequin, S.4    Traore, A.S.5
  • 42
    • 84973375251 scopus 로고    scopus 로고
    • Revealing a 5000-y-old beer recipe in China
    • Wang, J. et al. Revealing a 5000-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
  • 43
    • 84959213442 scopus 로고    scopus 로고
    • Revisiting Mortimer's Genome Renewal Hypothesis: Heterozygosity, homothallism, and the potential for adaptation in yeast
    • Magwene, P. M. Revisiting Mortimer's Genome Renewal Hypothesis: heterozygosity, homothallism, and the potential for adaptation in yeast. Adv. Exp. Med. Biol. 781, 37-48 (2014).
    • (2014) Adv. Exp. Med. Biol. , vol.781 , pp. 37-48
    • Magwene, P.M.1
  • 44
    • 84894574236 scopus 로고    scopus 로고
    • Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae
    • Plech, M., Visser, J. A. &Korona, R. Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae. G3 (Bethesda) 4, 315-323 (2014).
    • (2014) G3 (Bethesda) , vol.4 , pp. 315-323
    • Plech, M.1    Visser, J.A.2    Korona, R.3
  • 45
    • 84901239093 scopus 로고    scopus 로고
    • Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae
    • Hou, J., Friedrich, A., de Montigny, J. &Schacherer, J. Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae. Curr. Biol. 24, 1153-1159 (2014).
    • (2014) Curr. Biol. , vol.24 , pp. 1153-1159
    • Hou, J.1    Friedrich, A.2    De Montigny, J.3    Schacherer, J.4
  • 46
    • 33750437730 scopus 로고    scopus 로고
    • Sequence diversity, reproductive isolation and species concepts in Saccharomyces
    • Liti, G., Barton, D. B. &Louis, E. J. Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174, 839-850 (2006).
    • (2006) Genetics , vol.174 , pp. 839-850
    • Liti, G.1    Barton, D.B.2    Louis, E.J.3
  • 47
    • 78650160055 scopus 로고    scopus 로고
    • Flocculation in Saccharomyces cerevisiae: A review
    • Soares, E. V. Flocculation in Saccharomyces cerevisiae: a review. J. Appl. Microbiol. 110, 1-18 (2011).
    • (2011) J. Appl. Microbiol. , vol.110 , pp. 1-18
    • Soares, E.V.1
  • 48
    • 0037438569 scopus 로고    scopus 로고
    • Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae
    • Warringer, J. &Blomberg, A. Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast 20, 53-67 (2003).
    • (2003) Yeast , vol.20 , pp. 53-67
    • Warringer, J.1    Blomberg, A.2
  • 49
    • 51349167425 scopus 로고    scopus 로고
    • Chemogenetic fingerprinting by analysis of cellular growth dynamics
    • Warringer, J., Anevski, D., Liu, B. &Blomberg, A. Chemogenetic fingerprinting by analysis of cellular growth dynamics. BMC Chem. Biol. 8, 3 (2008).
    • (2008) BMC Chem. Biol. , vol.8 , pp. 3
    • Warringer, J.1    Anevski, D.2    Liu, B.3    Blomberg, A.4
  • 50
    • 0028933849 scopus 로고
    • Factors which affect the frequency of sporulation and tetrad formation in Saccharomyces cerevisiae baker's yeasts
    • Codón, A. C., Gasent-Ramirez, J. M. &Benitez, T. Factors which affect the frequency of sporulation and tetrad formation in Saccharomyces cerevisiae baker's yeasts. Appl. Environ. Microbiol. 61, 1677 (1995).
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 1677
    • Codón, A.C.1    Gasent-Ramirez, J.M.2    Benitez, T.3
  • 51
    • 70350397498 scopus 로고    scopus 로고
    • Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: Towards a new domesticated species
    • Albertin, W. et al. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J. Evol. Biol. 22, 2157-2170 (2009).
    • (2009) J. Evol. Biol. , vol.22 , pp. 2157-2170
    • Albertin, W.1
  • 53
    • 79551589417 scopus 로고    scopus 로고
    • HiTEC: Accurate error correction in highthroughput sequencing data
    • Ilie, L., Fazayeli, F. &Ilie, S. HiTEC: accurate error correction in highthroughput sequencing data. Bioinformatics 27, 295-302 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 295-302
    • Ilie, L.1    Fazayeli, F.2    Ilie, S.3
  • 54
    • 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
  • 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
    • 84914689868 scopus 로고    scopus 로고
    • Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
    • Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
    • (2014) PLoS ONE , vol.9 , pp. e112963
    • Walker, B.J.1
  • 57
    • 84862239242 scopus 로고    scopus 로고
    • A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
    • Swain, M. T. et al. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat. Protoc. 7, 1260-1284 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 1260-1284
    • Swain, M.T.1
  • 58
    • 23144444421 scopus 로고    scopus 로고
    • AUGUSTUS: A web server for gene prediction in eukaryotes that allows user-defined constraints
    • Stanke, M. &Morgenstern, B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33, W465-W467 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. W465-W467
    • Stanke, M.1    Morgenstern, B.2
  • 60
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie
    • Langmead, B. &Salzberg, S. L. Fast gapped-read alignment with Bowtie. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 61
    • 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
  • 62
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 63
    • 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
  • 64
    • 84903135724 scopus 로고    scopus 로고
    • Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing
    • Crauwels, S. et al. Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing. Appl. Environ. Microbiol. 80, 4398-4413 (2014).
    • (2014) Appl. Environ. Microbiol. , vol.80 , pp. 4398-4413
    • Crauwels, S.1
  • 65
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; Iso-2; iso-3
    • Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92 (2012).
    • (2012) Fly (Austin) , vol.6 , pp. 80-92
    • Cingolani, P.1
  • 66
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K. &Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 67
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and postanalysis of large phylogenies
    • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 68
    • 84897908606 scopus 로고    scopus 로고
    • Ignoring heterozygous sites biases phylogenomic estimates of divergence times: Implications for the evolutionary history of microtus voles
    • Lischer, H. E., Excoffier, L. &Heckel, G. Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles. Mol. Biol. Evol. 31, 817-831 (2013).
    • (2013) Mol. Biol. Evol. , vol.31 , pp. 817-831
    • Lischer, H.E.1    Excoffier, L.2    Heckel, G.3
  • 69
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: A Python library for phylogenetic computing
    • Sukumaran, J. &Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569-1571 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 70
    • 67649327176 scopus 로고    scopus 로고
    • FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
    • Price, M. N., Dehal, P. S. &Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641-1650 (2009).
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1641-1650
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 72
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: A tool set for whole-genome association and population-based linkage analyses
    • Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 559-575
    • Purcell, S.1
  • 73
    • 84859499806 scopus 로고    scopus 로고
    • EggLib: Processing, analysis and simulation tools for population genetics and genomics
    • De Mita, S. &Siol, M. EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genet. 13, 27 (2012).
    • (2012) BMC Genet. , vol.13 , pp. 27
    • De Mita, S.1    Siol, M.2
  • 74
    • 73449149044 scopus 로고    scopus 로고
    • Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
    • Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. &Bustamante, C. D. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695 (2009).
    • (2009) PLoS Genet. , vol.5 , pp. e1000695
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 75
    • 84930088928 scopus 로고    scopus 로고
    • Genetic isolation between two recently diverged populations of a symbiotic fungus
    • Branco, S. et al. Genetic isolation between two recently diverged populations of a symbiotic fungus. Mol. Ecol. 24, 2747-2758 (2015).
    • (2015) Mol. Ecol. , vol.24 , pp. 2747-2758
    • Branco, S.1
  • 76
    • 84861400043 scopus 로고    scopus 로고
    • Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
    • Klambauer, G. et al. cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res. 40, e69 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e69
    • Klambauer, G.1


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