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Volumn 8, Issue 1, 2021, Pages

The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis

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EID: 85107328966     PISSN: 20527276     EISSN: None     Source Type: Journal    
DOI: 10.1038/s41438-021-00565-4     Document Type: Article
Times cited : (39)

References (76)
  • 1
    • 85050664500 scopus 로고    scopus 로고
    • Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer
    • COI: 1:CAS:528:DC%2BC1cXhtlClsLjE, PID: 30022161
    • Wu, D. et al. Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer. Nature 559, 637–641 (2018). DOI: 10.1038/s41586-018-0350-5
    • (2018) Nature , vol.559 , pp. 637-641
    • Wu, D.1
  • 2
    • 85069515484 scopus 로고    scopus 로고
    • Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientationsCrystallizing sugar science
    • Yang, T. et al. Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientationsCrystallizing sugar science. Nat. Commun. 10, 3214 (2019).
    • (2019) Nat. Commun. , vol.10 , pp. 3214
    • Yang, T.1
  • 3
    • 84879634195 scopus 로고    scopus 로고
    • Steviol glycosides: chemical diversity, metabolism, and function
    • COI: 1:CAS:528:DC%2BC3sXosVeit74%3D, PID: 23713723
    • Ceunen, S. & Geuns, J. M. Steviol glycosides: chemical diversity, metabolism, and function. J. Nat. Prod. 76, 1201–1228 (2013). DOI: 10.1021/np400203b
    • (2013) J. Nat. Prod. , vol.76 , pp. 1201-1228
    • Ceunen, S.1    Geuns, J.M.2
  • 4
    • 79551469898 scopus 로고    scopus 로고
    • A review on the improvement of stevia [Stevia rebaudiana (Bertoni)]
    • Yadav, A. K., Singh, S., Dhyani, D. & Ahuja, P. S. A review on the improvement of stevia [Stevia rebaudiana (Bertoni)]. Can. J. Plant Sci. 91, 1–27 (2011). DOI: 10.4141/cjps10086
    • (2011) Can. J. Plant Sci. , vol.91 , pp. 1-27
    • Yadav, A.K.1    Singh, S.2    Dhyani, D.3    Ahuja, P.S.4
  • 5
    • 57749106147 scopus 로고    scopus 로고
    • Stevioside and related compounds: therapeutic benefits beyond sweetness
    • COI: 1:CAS:528:DC%2BD1cXhsFagtrrI, PID: 19000919
    • Chatsudthipong, V. & Muanprasat, C. Stevioside and related compounds: therapeutic benefits beyond sweetness. Pharmacol. Ther. 121, 41–54 (2009). DOI: 10.1016/j.pharmthera.2008.09.007
    • (2009) Pharmacol. Ther. , vol.121 , pp. 41-54
    • Chatsudthipong, V.1    Muanprasat, C.2
  • 6
    • 85016619279 scopus 로고    scopus 로고
    • Steviol glycosides enhance pancreatic beta-cell function and taste sensation by potentiation of TRPM5 channel activity
    • COI: 1:CAS:528:DC%2BC2sXlsV2ju70%3D, PID: 28361903
    • Philippaert, K. et al. Steviol glycosides enhance pancreatic beta-cell function and taste sensation by potentiation of TRPM5 channel activity. Nat. Commun. 8, 14733 (2017). DOI: 10.1038/ncomms14733
    • (2017) Nat. Commun. , vol.8
    • Philippaert, K.1
  • 7
    • 84879819621 scopus 로고    scopus 로고
    • Diterpene glycosides from Stevia phlebophylla A. Gray
    • COI: 1:CAS:528:DC%2BC3sXhtlOru73P, PID: 23831634
    • Ceunen, S. et al. Diterpene glycosides from Stevia phlebophylla A. Gray. Carbohydr. Res. 379, 1–6 (2013). DOI: 10.1016/j.carres.2013.06.003
    • (2013) Carbohydr. Res. , vol.379 , pp. 1-6
    • Ceunen, S.1
  • 8
    • 0032441205 scopus 로고    scopus 로고
    • Stevia rebaudiana: Its agricultural, biological, and chemical properties
    • COI: 1:CAS:528:DyaK1MXks1amtg%3D%3D
    • Brandle, J. E., Starratt, A. N. & Gijzen, M. Stevia rebaudiana: Its agricultural, biological, and chemical properties. Can. J. Plant Sci. 78, 527–536 (1998). DOI: 10.4141/P97-114
    • (1998) Can. J. Plant Sci. , vol.78 , pp. 527-536
    • Brandle, J.E.1    Starratt, A.N.2    Gijzen, M.3
  • 9
    • 0142058124 scopus 로고    scopus 로고
    • Stevioside
    • COI: 1:CAS:528:DC%2BD3sXotVeqsL4%3D, PID: 14561506
    • Geuns, J. M. C. Stevioside. Phytochemistry 64, 913–921 (2003). DOI: 10.1016/S0031-9422(03)00426-6
    • (2003) Phytochemistry , vol.64 , pp. 913-921
    • Geuns, J.M.C.1
  • 10
    • 84856221678 scopus 로고    scopus 로고
    • Stevia rebaudiana Bertoni, source of a high-potency natural sweetener: a comprehensive review on the biochemical, nutritional and functional aspects
    • COI: 1:CAS:528:DC%2BC38XhsFKisLo%3D, PID: 29243591
    • Lemus-Mondaca, R., Vega-Gálvez, A., Zura-Bravo, L. & Ah-Hen, K. Stevia rebaudiana Bertoni, source of a high-potency natural sweetener: a comprehensive review on the biochemical, nutritional and functional aspects. Food Chem. 132, 1121–1132 (2012). DOI: 10.1016/j.foodchem.2011.11.140
    • (2012) Food Chem. , vol.132 , pp. 1121-1132
    • Lemus-Mondaca, R.1    Vega-Gálvez, A.2    Zura-Bravo, L.3    Ah-Hen, K.4
  • 11
    • 84896505520 scopus 로고    scopus 로고
    • Methylerythritol and mevalonate pathway contributions to biosynthesis of mono-, sesqui-, and diterpenes in glandular trichomes and leaves of Stevia rebaudiana Bertoni
    • PID: 24579920, COI: 1:CAS:528:DC%2BC2cXjtlOks78%3D
    • Wolwer-Rieck, U., May, B., Lankes, C. & Wust, M. Methylerythritol and mevalonate pathway contributions to biosynthesis of mono-, sesqui-, and diterpenes in glandular trichomes and leaves of Stevia rebaudiana Bertoni. J. Agric. Food Chem. 62, 2428–2435 (2014). DOI: 10.1021/jf500270s
    • (2014) J. Agric. Food Chem. , vol.62 , pp. 2428-2435
    • Wolwer-Rieck, U.1    May, B.2    Lankes, C.3    Wust, M.4
  • 12
    • 0033180217 scopus 로고    scopus 로고
    • Diterpene synthesis in Stevia rebaudiana: recruitment and up-regulation of key enzymes from the gibberellin biosynthetic pathway
    • COI: 1:CAS:528:DyaK1MXms1Srur8%3D, PID: 10504563
    • Richman, A. S. et al. Diterpene synthesis in Stevia rebaudiana: recruitment and up-regulation of key enzymes from the gibberellin biosynthetic pathway. Plant J. 19, 411–421 (1999). DOI: 10.1046/j.1365-313X.1999.00531.x
    • (1999) Plant J. , vol.19 , pp. 411-421
    • Richman, A.S.1
  • 13
    • 33745189198 scopus 로고    scopus 로고
    • Spatial organisation of four enzymes from Stevia rebaudiana that are involved in steviol glycoside synthesis
    • COI: 1:CAS:528:DC%2BD28XlvFaisbk%3D, PID: 16786291
    • Humphrey, T. V., Richman, A. S., Menassa, R. & Brandle, J. E. Spatial organisation of four enzymes from Stevia rebaudiana that are involved in steviol glycoside synthesis. Plant Mol. Biol. 61, 47–62 (2006). DOI: 10.1007/s11103-005-5966-9
    • (2006) Plant Mol. Biol. , vol.61 , pp. 47-62
    • Humphrey, T.V.1    Richman, A.S.2    Menassa, R.3    Brandle, J.E.4
  • 14
    • 34447101720 scopus 로고    scopus 로고
    • Steviol glycoside biosynthesis
    • COI: 1:CAS:528:DC%2BD2sXnslGmu7k%3D, PID: 17397883
    • Brandle, J. E. & Telmer, P. G. Steviol glycoside biosynthesis. Phytochemistry 68, 1855–1863 (2007). DOI: 10.1016/j.phytochem.2007.02.010
    • (2007) Phytochemistry , vol.68 , pp. 1855-1863
    • Brandle, J.E.1    Telmer, P.G.2
  • 15
    • 0030586753 scopus 로고    scopus 로고
    • Hydroxylation of ent-kaurenoic acid to steviol in Stevia rebaudiana Bertoni-purification and partial characterization of the enzyme
    • COI: 1:CAS:528:DyaK28XltVSntb4%3D, PID: 8806729
    • Kim, K. K., Sawa, Y. & Shibata, H. Hydroxylation of ent-kaurenoic acid to steviol in Stevia rebaudiana Bertoni-purification and partial characterization of the enzyme. Arch. Biochem. Biophys. 332, 223–230 (1996). DOI: 10.1006/abbi.1996.0336
    • (1996) Arch. Biochem. Biophys. , vol.332 , pp. 223-230
    • Kim, K.K.1    Sawa, Y.2    Shibata, H.3
  • 16
    • 84899764072 scopus 로고    scopus 로고
    • To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism
    • COI: 1:CAS:528:DC%2BC2cXhtFWhtrvN, PID: 24471837
    • Zi, J. C., Mafu, S. & Peters, R. J. To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism. Annu. Rev. Plant Biol. 65, 259–286 (2014). DOI: 10.1146/annurev-arplant-050213-035705
    • (2014) Annu. Rev. Plant Biol. , vol.65 , pp. 259-286
    • Zi, J.C.1    Mafu, S.2    Peters, R.J.3
  • 17
    • 44949108257 scopus 로고    scopus 로고
    • Gibberellin metabolism and its regulation
    • COI: 1:CAS:528:DC%2BD1cXntFaqsLg%3D, PID: 18173378
    • Yamaguchi, S. Gibberellin metabolism and its regulation. Annu. Rev. Plant Biol. 59, 225–251 (2008). DOI: 10.1146/annurev.arplant.59.032607.092804
    • (2008) Annu. Rev. Plant Biol. , vol.59 , pp. 225-251
    • Yamaguchi, S.1
  • 18
    • 84859267599 scopus 로고    scopus 로고
    • UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin in Gardenia jasminoides
    • COI: 1:CAS:528:DC%2BC38XksFeitLg%3D, PID: 22569263
    • Nagatoshi, M. et al. UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin in Gardenia jasminoides. FEBS Lett. 586, 1055–1061 (2012). DOI: 10.1016/j.febslet.2012.03.003
    • (2012) FEBS Lett. , vol.586 , pp. 1055-1061
    • Nagatoshi, M.1
  • 19
    • 85053939715 scopus 로고    scopus 로고
    • Diterpenoid UDP-Glycosyltransferases from Chinese Sweet Tea and Ashitaba Complete the Biosynthesis of Rubusoside
    • COI: 1:CAS:528:DC%2BC1cXht1yitrbP, PID: 29885474
    • Sun, Y. et al. Diterpenoid UDP-Glycosyltransferases from Chinese Sweet Tea and Ashitaba Complete the Biosynthesis of Rubusoside. Mol. Plant 11, 1308–1311 (2018). DOI: 10.1016/j.molp.2018.05.010
    • (2018) Mol. Plant , vol.11 , pp. 1308-1311
    • Sun, Y.1
  • 20
    • 0036836919 scopus 로고    scopus 로고
    • Leaf Ests from Stevia rebaudiana: a resource for gene discovery in diterpene synthesis
    • COI: 1:CAS:528:DC%2BD38Xms1ektr0%3D, PID: 12374295
    • Brandle, J. E., Richman, A., Swanson, A. K. & Chapman, B. P. Leaf Ests from Stevia rebaudiana: a resource for gene discovery in diterpene synthesis. Plant Mol. Biol. 50, 613–622 (2002). DOI: 10.1023/A:1019993221986
    • (2002) Plant Mol. Biol. , vol.50 , pp. 613-622
    • Brandle, J.E.1    Richman, A.2    Swanson, A.K.3    Chapman, B.P.4
  • 21
    • 12744278046 scopus 로고    scopus 로고
    • Functional genomics uncovers three glucosyltransferases involved in the synthesis of the major sweet glucosides of Stevia rebaudiana
    • COI: 1:CAS:528:DC%2BD2MXhtVWjsLY%3D
    • Richman, A. et al. Functional genomics uncovers three glucosyltransferases involved in the synthesis of the major sweet glucosides of Stevia rebaudiana. Plant J. 41, 56–67 (2004). DOI: 10.1111/j.1365-313X.2004.02275.x
    • (2004) Plant J. , vol.41 , pp. 56-67
    • Richman, A.1
  • 22
    • 84890034912 scopus 로고    scopus 로고
    • Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
    • COI: 1:CAS:528:DC%2BC3sXhslWjtLvM, PID: 24185095
    • Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013). DOI: 10.1038/nbt.2727
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1119-1125
    • Burton, J.N.1
  • 23
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
    • PID: 26059717, COI: 1:CAS:528:DC%2BC28Xht1Cit7fN
    • Simão, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). DOI: 10.1093/bioinformatics/btv351
    • (2015) Bioinformatics , vol.31 , pp. 3210-3212
    • Simão, F.A.1
  • 24
    • 85020219786 scopus 로고    scopus 로고
    • The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
    • COI: 1:CAS:528:DC%2BC2sXosVagtL4%3D, PID: 28538728
    • Badouin, H. et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 546, 148–152 (2017). DOI: 10.1038/nature22380
    • (2017) Nature , vol.546 , pp. 148-152
    • Badouin, H.1
  • 25
    • 85017430250 scopus 로고    scopus 로고
    • Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
    • COI: 1:CAS:528:DC%2BC2sXmtFCrsLk%3D, PID: 28401891
    • Reyes-Chin-Wo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8, 14953 (2017). DOI: 10.1038/ncomms14953
    • (2017) Nat. Commun. , vol.8
    • Reyes-Chin-Wo, S.1
  • 26
    • 85057117212 scopus 로고    scopus 로고
    • The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits
    • COI: 1:CAS:528:DC%2BC1cXit1ehs7%2FI
    • Song, C. et al. The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits. Mol. Plant 11, 1482–1491 (2018). DOI: 10.1016/j.molp.2018.10.003
    • (2018) Mol. Plant , vol.11 , pp. 1482-1491
    • Song, C.1
  • 27
    • 84949228107 scopus 로고    scopus 로고
    • Polyploidy and genome evolution in plants
    • COI: 1:CAS:528:DC%2BC2MXhvVOqsLrP, PID: 26656231
    • Soltis, P. S., Marchant, D. B., Van de Peer, Y. & Soltis, D. E. Polyploidy and genome evolution in plants. Curr. Opin. Genet. Dev. 35, 119–125 (2015). DOI: 10.1016/j.gde.2015.11.003
    • (2015) Curr. Opin. Genet. Dev. , vol.35 , pp. 119-125
    • Soltis, P.S.1    Marchant, D.B.2    Van de Peer, Y.3    Soltis, D.E.4
  • 28
    • 84962437293 scopus 로고    scopus 로고
    • Ancient WGD events as drivers of key innovations in angiosperms
    • PID: 27064530
    • Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Plant. Biol. 30, 159–165 (2016). DOI: 10.1016/j.pbi.2016.03.015
    • (2016) Curr. Opin. Plant. Biol. , vol.30 , pp. 159-165
    • Soltis, P.S.1    Soltis, D.E.2
  • 29
    • 60249085527 scopus 로고    scopus 로고
    • Polyploidy and angiosperm diversification
    • PID: 21628192
    • Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). DOI: 10.3732/ajb.0800079
    • (2009) Am. J. Bot. , vol.96 , pp. 336-348
    • Soltis, D.E.1
  • 30
    • 84860137835 scopus 로고    scopus 로고
    • MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
    • COI: 1:CAS:528:DC%2BC38Xls1SmsL0%3D, PID: 22217600
    • Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012). DOI: 10.1093/nar/gkr1293
    • (2012) Nucleic Acids Res. , vol.40
    • Wang, Y.1
  • 31
    • 84982980319 scopus 로고    scopus 로고
    • Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae
    • COI: 1:CAS:528:DC%2BC1cXkslGltrc%3D, PID: 27313199
    • Barker, M. S. et al. Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae. Am. J. Bot. 103, 1203–1211 (2016). DOI: 10.3732/ajb.1600113
    • (2016) Am. J. Bot. , vol.103 , pp. 1203-1211
    • Barker, M.S.1
  • 32
    • 84862777561 scopus 로고    scopus 로고
    • A genome triplication associated with early diversification of the core eudicots
    • PID: 22280555
    • Jiao, Y. et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13, R3 (2012). DOI: 10.1186/gb-2012-13-1-r3
    • (2012) Genome Biol. , vol.13
    • Jiao, Y.1
  • 33
    • 84155180843 scopus 로고    scopus 로고
    • A comprehensive analysis of fifteen genes of steviol glycosides biosynthesis pathway in Stevia rebaudiana (Bertoni)
    • COI: 1:CAS:528:DC%2BC3MXhs1Krur3K, PID: 22037480
    • Kumar, H. et al. A comprehensive analysis of fifteen genes of steviol glycosides biosynthesis pathway in Stevia rebaudiana (Bertoni). Gene 492, 276–284 (2012). DOI: 10.1016/j.gene.2011.10.015
    • (2012) Gene , vol.492 , pp. 276-284
    • Kumar, H.1
  • 34
    • 57749092770 scopus 로고    scopus 로고
    • Peroxisomal localization of Arabidopsis isopentenyl diphosphate isomerases suggests that part of the plant isoprenoid mevalonic acid pathway is compartmentalized to peroxisomes
    • COI: 1:CAS:528:DC%2BD1cXhsVSnurvN, PID: 18988695
    • Sapir-Mir, M. et al. Peroxisomal localization of Arabidopsis isopentenyl diphosphate isomerases suggests that part of the plant isoprenoid mevalonic acid pathway is compartmentalized to peroxisomes. Plant Physiol. 148, 1219–1228 (2008). DOI: 10.1104/pp.108.127951
    • (2008) Plant Physiol. , vol.148 , pp. 1219-1228
    • Sapir-Mir, M.1
  • 35
    • 84957429577 scopus 로고    scopus 로고
    • Pathway mining-based integration of critical enzyme parts for de novo biosynthesis of steviolglycosides sweetener in Escherichia coli
    • PID: 26358188
    • Wang, J., Li, S., Xiong, Z. & Wang, Y. Pathway mining-based integration of critical enzyme parts for de novo biosynthesis of steviolglycosides sweetener in Escherichia coli. Cell Res. 26, 258–261 (2016). DOI: 10.1038/cr.2015.111
    • (2016) Cell Res. , vol.26 , pp. 258-261
    • Wang, J.1    Li, S.2    Xiong, Z.3    Wang, Y.4
  • 36
    • 84887979276 scopus 로고    scopus 로고
    • Functional analysis of Arabidopsis CYP714A1 and CYP714A2 reveals that they are distinct gibberellin modification enzymes
    • COI: 1:CAS:528:DC%2BC3sXhslWrurfI, PID: 24009336
    • Nomura, T. et al. Functional analysis of Arabidopsis CYP714A1 and CYP714A2 reveals that they are distinct gibberellin modification enzymes. Plant Cell Physiol. 54, 1837–1851 (2013). DOI: 10.1093/pcp/pct125
    • (2013) Plant Cell Physiol. , vol.54 , pp. 1837-1851
    • Nomura, T.1
  • 37
    • 84865504323 scopus 로고    scopus 로고
    • Sugar substitutes: health controversy over perceived benefits
    • COI: 1:CAS:528:DC%2BC3MXhsFKqtLfK, PID: 22025850
    • Tandel, K. R. Sugar substitutes: health controversy over perceived benefits. J. Pharmacol. Pharmacother. 2, 236 (2011). DOI: 10.4103/0976-500X.85936
    • (2011) J. Pharmacol. Pharmacother. , vol.2 , pp. 236
    • Tandel, K.R.1
  • 38
    • 84883183253 scopus 로고    scopus 로고
    • Artificial sweeteners produce the counterintuitive effect of inducing metabolic derangements
    • COI: 1:CAS:528:DC%2BC3sXhtVyqt7%2FO, PID: 23850261
    • Swithers, S. E. Artificial sweeteners produce the counterintuitive effect of inducing metabolic derangements. Trends Endocrinol. Metab. 24, 431–441 (2013). DOI: 10.1016/j.tem.2013.05.005
    • (2013) Trends Endocrinol. Metab. , vol.24 , pp. 431-441
    • Swithers, S.E.1
  • 39
    • 85096404723 scopus 로고    scopus 로고
    • The complete genome sequence of Stevia rebaudiana, the Sweetleaf
    • PID: 33299551
    • O’Neill, K. & Pirro, S. The complete genome sequence of Stevia rebaudiana, the Sweetleaf. F1000Research. 9, 751 (2020). DOI: 10.12688/f1000research.24396.1
    • (2020) F1000Research. , vol.9 , pp. 751
    • O’Neill, K.1    Pirro, S.2
  • 40
    • 84907342844 scopus 로고    scopus 로고
    • Doubling down on genomes: polyploidy and crop plants
    • PID: 25090999
    • Renny-Byfield, S. & Wendel, J. F. Doubling down on genomes: polyploidy and crop plants. Am. J. Bot. 101, 1711–1725 (2014). DOI: 10.3732/ajb.1400119
    • (2014) Am. J. Bot. , vol.101 , pp. 1711-1725
    • Renny-Byfield, S.1    Wendel, J.F.2
  • 41
    • 84982899807 scopus 로고    scopus 로고
    • Evolution of gene duplication in plants
    • COI: 1:CAS:528:DC%2BC28XhvFKlsr%2FN, PID: 27288366
    • Panchy, N., Lehti-Shiu, M. & Shiu, S. H. Evolution of gene duplication in plants. Plant Physiol. 171, 2294–2316 (2016). DOI: 10.1104/pp.16.00523
    • (2016) Plant Physiol. , vol.171 , pp. 2294-2316
    • Panchy, N.1    Lehti-Shiu, M.2    Shiu, S.H.3
  • 42
    • 85019066712 scopus 로고    scopus 로고
    • Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    • COI: 1:CAS:528:DC%2BC2sXhtFyjsrvI, PID: 5411767
    • Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017). DOI: 10.1101/gr.215087.116
    • (2017) Genome Res. , vol.27 , pp. 722-736
    • Koren, S.1
  • 43
    • 84991694364 scopus 로고    scopus 로고
    • Phased diploid genome assembly with single-molecule real-time sequencing
    • COI: 1:CAS:528:DC%2BC28Xhs1ykur7K, PID: 27749838
    • Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016). DOI: 10.1038/nmeth.4035
    • (2016) Nat. Methods , vol.13 , pp. 1050-1054
    • Chin, C.S.1
  • 44
    • 84994899573 scopus 로고    scopus 로고
    • Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage
    • PID: 27458204, COI: 1:CAS:528:DC%2BC2sXhtV2itrbN
    • Chakraborty, M., Baldwin-Brown, J. G., Long, A. D. & Emerson, J. J. Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 44, e147 (2016). DOI: 10.1093/nar/gkw419
    • (2016) Nucleic Acids Res. , vol.44
    • Chakraborty, M.1    Baldwin-Brown, J.G.2    Long, A.D.3    Emerson, J.J.4
  • 45
    • 84914689868 scopus 로고    scopus 로고
    • Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement
    • PID: 25409509, COI: 1:CAS:528:DC%2BC2MXisFCmurk%3D
    • Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014). DOI: 10.1371/journal.pone.0112963
    • (2014) PLoS ONE , vol.9
    • Walker, B.J.1
  • 46
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • COI: 1:CAS:528:DC%2BD1MXot1Cjtbo%3D, PID: 2705234
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). DOI: 10.1093/bioinformatics/btp324
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 47
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    • COI: 1:CAS:528:DC%2BD2sXmtVKqur8%3D, PID: 17332020
    • Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067 (2007). DOI: 10.1093/bioinformatics/btm071
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 48
    • 84870379849 scopus 로고    scopus 로고
    • Hi-C: A comprehensive technique to capture the conformation of genomes
    • COI: 1:CAS:528:DC%2BC38XhtVyksbjO, PID: 22652625
    • Belton, J. M. et al. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods 58, 268–276 (2012). DOI: 10.1016/j.ymeth.2012.05.001
    • (2012) Methods , vol.58 , pp. 268-276
    • Belton, J.M.1
  • 49
    • 84952861819 scopus 로고    scopus 로고
    • HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
    • PID: 26619908, COI: 1:CAS:528:DC%2BC28XntV2iurg%3D
    • Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015). DOI: 10.1186/s13059-015-0831-x
    • (2015) Genome Biol. , vol.16
    • Servant, N.1
  • 50
    • 84860513986 scopus 로고    scopus 로고
    • PILER: identification and classification of genomic repeats
    • Edgar, R. C. & Myers, E. W. PILER: identification and classification of genomic repeats. Bioinformatics 21, 152–158 (2005). DOI: 10.1093/bioinformatics/bti1003
    • (2005) Bioinformatics , vol.21 , pp. 152-158
    • Edgar, R.C.1    Myers, E.W.2
  • 51
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, 351–358 (2005). DOI: 10.1093/bioinformatics/bti1018
    • (2005) Bioinformatics , vol.21 , pp. 351-358
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 52
    • 34547592867 scopus 로고    scopus 로고
    • LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
    • PID: 17485477
    • Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007). DOI: 10.1093/nar/gkm286
    • (2007) Nucleic Acids Res. , vol.35 , pp. W265-W268
    • Xu, Z.1    Wang, H.2
  • 53
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • COI: 1:CAS:528:DC%2BD2sXhtlajtrnF, PID: 17984973
    • Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982 (2007). DOI: 10.1038/nrg2165
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 973-982
    • Wicker, T.1
  • 54
    • 63049126614 scopus 로고    scopus 로고
    • Using RepeatMasker to identify repetitive elements in genomic sequences
    • Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinforma. 25, 4.10.1–4.10.14 (2009). DOI: 10.1002/0471250953.bi0410s25
    • (2009) Curr. Protoc. Bioinforma. , vol.25 , pp. 4.10.1-4.10.14
    • Tarailo-Graovac, M.1    Chen, N.2
  • 55
    • 23844525077 scopus 로고    scopus 로고
    • Repbase Update, a database of eukaryotic repetitive elements
    • COI: 1:STN:280:DC%2BD2Mvislertw%3D%3D, PID: 16093699
    • Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110, 462–467 (2005). DOI: 10.1159/000084979
    • (2005) Cytogenet Genome Res. , vol.110 , pp. 462-467
    • Jurka, J.1
  • 56
    • 3242889577 scopus 로고    scopus 로고
    • AUGUSTUS: a web server for gene finding in eukaryotes
    • COI: 1:CAS:528:DC%2BD2cXlvFKntLg%3D, PID: 15215400
    • Stanke, M., Steinkamp, R., Waack, S. & Morgenstern, B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32, W309–W312 (2004). DOI: 10.1093/nar/gkh379
    • (2004) Nucleic Acids Res. , vol.32 , pp. W309-W312
    • Stanke, M.1    Steinkamp, R.2    Waack, S.3    Morgenstern, B.4
  • 57
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    • COI: 1:CAS:528:DC%2BD2cXhtVSru77E, PID: 15145805
    • Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004). DOI: 10.1093/bioinformatics/bth315
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 58
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: predict effect of non-synonymous polymorphisms on function
    • COI: 1:CAS:528:DC%2BD2sXosFSnu7o%3D, PID: 17526529
    • Bromberg, Y. & Rost, B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 35, 3823–3835 (2007). DOI: 10.1093/nar/gkm238
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 60
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • COI: 1:CAS:528:DyaK3MXitVGmsA%3D%3D, PID: 2231712
    • Altschul, S. F. et al. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). DOI: 10.1016/S0022-2836(05)80360-2
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 61
    • 84970006552 scopus 로고    scopus 로고
    • Using intron position conservation for homology-based gene prediction
    • PID: 26893356, COI: 1:CAS:528:DC%2BC28XhsFSisLjO
    • Keilwagen, J. et al. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 44, e89 (2016). DOI: 10.1093/nar/gkw092
    • (2016) Nucleic Acids Res. , vol.44
    • Keilwagen, J.1
  • 62
    • 84942117101 scopus 로고    scopus 로고
    • Identification of protein coding regions in RNA transcripts
    • PID: 25870408, COI: 1:CAS:528:DC%2BC2MXhsFSrtb7O
    • Tang, S., Lomsadze, A. & Borodovsky, M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 43, e78 (2015). DOI: 10.1093/nar/gkv227
    • (2015) Nucleic Acids Res. , vol.43
    • Tang, S.1    Lomsadze, A.2    Borodovsky, M.3
  • 63
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    • PID: 18190707, COI: 1:CAS:528:DC%2BD1cXjvVWkt7o%3D
    • Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008). DOI: 10.1186/gb-2008-9-1-r7
    • (2008) Genome Biol. , vol.9
    • Haas, B.J.1
  • 64
    • 33846573830 scopus 로고    scopus 로고
    • Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    • PID: 17194304, COI: 1:CAS:528:DC%2BD2sXhtFajsb4%3D
    • Campbell, M. A. et al. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7, 327 (2006). DOI: 10.1186/1471-2164-7-327
    • (2006) BMC Genomics , vol.7
    • Campbell, M.A.1
  • 65
    • 0037255072 scopus 로고    scopus 로고
    • The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    • COI: 1:CAS:528:DC%2BD3sXhvFSmtL0%3D, PID: 12520024
    • Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003). DOI: 10.1093/nar/gkg095
    • (2003) Nucleic Acids Res. , vol.31 , pp. 365-370
    • Boeckmann, B.1
  • 66
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    • COI: 1:CAS:528:DC%2BD2MXpvFGqt70%3D
    • Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676 (2005). DOI: 10.1093/bioinformatics/bti610
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1
  • 67
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • COI: 1:CAS:528:DC%2BD3cXjtFSlsbc%3D, PID: 10802651
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000). DOI: 10.1038/75556
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 68
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • COI: 1:CAS:528:DC%2BD3cXhvVGqu74%3D, PID: 102409
    • Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000). DOI: 10.1093/nar/28.1.27
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 69
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • COI: 1:CAS:528:DC%2BD3sXnslKhtLk%3D, PID: 403725
    • Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003). DOI: 10.1101/gr.1224503
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 70
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • COI: 1:CAS:528:DC%2BC3sXksFWisLc%3D, PID: 23329690
    • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013). DOI: 10.1093/molbev/mst010
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 71
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • COI: 1:CAS:528:DC%2BD3cXisVSgt7g%3D, PID: 10742046
    • Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000). DOI: 10.1093/oxfordjournals.molbev.a026334
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 72
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • COI: 1:CAS:528:DC%2BD28XhtFKlsbfI
    • Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006). DOI: 10.1093/bioinformatics/btl446
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 73
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • COI: 1:CAS:528:DC%2BD2sXpsVGrs7c%3D
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). DOI: 10.1093/molbev/msm088
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 74
    • 33646856440 scopus 로고    scopus 로고
    • CAFE: a computational tool for the study of gene family evolution
    • COI: 1:CAS:528:DC%2BD28Xktlarsrc%3D
    • De Bie, T. et al. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269–1271 (2006). DOI: 10.1093/bioinformatics/btl097
    • (2006) Bioinformatics , vol.22 , pp. 1269-1271
    • De Bie, T.1
  • 75
    • 85088293993 scopus 로고    scopus 로고
    • TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data
    • COI: 1:CAS:528:DC%2BB3cXhsVCltLzE, PID: 32585190
    • Chen, C. et al. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant 13, 1194–1202 (2020). DOI: 10.1016/j.molp.2020.06.009
    • (2020) Mol. Plant , vol.13 , pp. 1194-1202
    • Chen, C.1
  • 76
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • COI: 1:CAS:528:DC%2BD1MXhtFCjsLvJ, PID: 19541911
    • Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009). DOI: 10.1101/gr.092759.109
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1


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