메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery

Author keywords

de novo transcriptome assembly; Forest genomics; Functional annotation; Nothofagaceae; Pyrosequencing; SSRs

Indexed keywords

COMPLEMENTARY DNA; MOLECULAR MARKER; TRANSCRIPTOME;

EID: 84863109050     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-291     Document Type: Article
Times cited : (23)

References (45)
  • 1
    • 77952743918 scopus 로고    scopus 로고
    • Nothofagus betuloides (Mirb.) Oerst 1871 (Fagales: Nothofagaceae) Forests in southern Patagonia and Tierra del Fuego
    • Promis A, Cruz G, Reif A, Gartner S. Nothofagus betuloides (Mirb.) Oerst 1871 (Fagales: Nothofagaceae) Forests in southern Patagonia and Tierra del Fuego. Anales Instituto Patagonia (Chile) 2008, 36(1):53-68.
    • (2008) Anales Instituto Patagonia (Chile) , vol.36 , Issue.1 , pp. 53-68
    • Promis, A.1    Cruz, G.2    Reif, A.3    Gartner, S.4
  • 2
    • 84876199994 scopus 로고    scopus 로고
    • Orientación Gráfica Editora, Buenos Aires, Stella RA, Ottone JR, 2, In Maderas y Bosques Argentinos. Volume 2
    • Guerra PE. Especies nativas o autóctonas de los Bosques subantárticos 2009, 975-1009. Orientación Gráfica Editora, Buenos Aires, Stella RA, Ottone JR, 2, In Maderas y Bosques Argentinos. Volume 2.
    • (2009) Especies nativas o autóctonas de los Bosques subantárticos , pp. 975-1009
    • Guerra, P.E.1
  • 3
    • 0001760051 scopus 로고
    • Nothofagus nervosa (Phil.) Dim. et Mil. The correct name for raulí, a chilean southern beech (N. procera)
    • Lennon JA, Martin ES, Steven RA, Wingston DL. Nothofagus nervosa (Phil.) Dim. et Mil. The correct name for raulí, a chilean southern beech (N. procera). Arboricul 1987, 11:323-332.
    • (1987) Arboricul , vol.11 , pp. 323-332
    • Lennon, J.A.1    Martin, E.S.2    Steven, R.A.3    Wingston, D.L.4
  • 4
    • 0031720590 scopus 로고    scopus 로고
    • Chloroplast DNA markers reveal a geographical divide across Argentinean southern beech Nothofagus nervosa(Phil.) Dim. et Mil. distribution area
    • Marchelli P, Gallo L, Scholz F, Ziegenhagen B. Chloroplast DNA markers reveal a geographical divide across Argentinean southern beech Nothofagus nervosa(Phil.) Dim. et Mil. distribution area. TheorAppl Genet 1998, 97:642-646.
    • (1998) TheorAppl Genet , vol.97 , pp. 642-646
    • Marchelli, P.1    Gallo, L.2    Scholz, F.3    Ziegenhagen, B.4
  • 5
    • 0004101735 scopus 로고
    • Editorial Universitaria, Santiago de Chile, Variación, Estructura y Dinámica
    • Donoso C. Bosques templados de Chile y Argentina 1993, Editorial Universitaria, Santiago de Chile, Variación, Estructura y Dinámica.
    • (1993) Bosques templados de Chile y Argentina
    • Donoso, C.1
  • 7
    • 0033598211 scopus 로고    scopus 로고
    • Annual and geographic variation in seed traits of Argentinean populations of southern beech Nothofagus nervosa (Phil.) Dim. et Mil
    • Marchelli P, Gallo L. Annual and geographic variation in seed traits of Argentinean populations of southern beech Nothofagus nervosa (Phil.) Dim. et Mil . Forest Ecol Manag 1999, 121:239-250.
    • (1999) Forest Ecol Manag , vol.121 , pp. 239-250
    • Marchelli, P.1    Gallo, L.2
  • 9
    • 78751550555 scopus 로고    scopus 로고
    • Forest tree genomics: growing resources and applications
    • Neale DB, Kremer A. Forest tree genomics: growing resources and applications. Nat Rev Genet 2011, 12:111-122.
    • (2011) Nat Rev Genet , vol.12 , pp. 111-122
    • Neale, D.B.1    Kremer, A.2
  • 11
    • 48249125753 scopus 로고    scopus 로고
    • Grattapaglia D, Sederoff R, Kirst M: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    • 10.1186/1471-2164-9-312, 2483731, 18590545
    • Novaes E, Drost DR, Farmerie WG, Pappas GJ. Grattapaglia D, Sederoff R, Kirst M: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
    • (2008) BMC Genomics , vol.9 , pp. 312
    • Novaes, E.1    Drost, D.R.2    Farmerie, W.G.3    Pappas, G.J.4
  • 12
    • 78649501801 scopus 로고    scopus 로고
    • De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq
    • 10.1186/1471-2164-11-681, 3053591, 21122097
    • Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 2010, 11:681. 10.1186/1471-2164-11-681, 3053591, 21122097.
    • (2010) BMC Genomics , vol.11 , pp. 681
    • Mizrachi, E.1    Hefer, C.A.2    Ranik, M.3    Joubert, F.4    Myburg, A.A.5
  • 14
    • 60549112895 scopus 로고    scopus 로고
    • Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiate D
    • Li XG, Wu HX, Dillon SK, Southerton SG. Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiate D. Don. BMC Genomics 2009, 10:41.
    • (2009) Don. BMC Genomics , vol.10 , pp. 41
    • Li, X.G.1    Wu, H.X.2    Dillon, S.K.3    Southerton, S.G.4
  • 16
    • 12544255680 scopus 로고    scopus 로고
    • Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves
    • 10.1093/pcp/pci009, 15653793
    • Nanjo T, Futamura N, Nishiguchi M, Igasaki T, Shinozaki K, Shinohara K. Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol 2004, 45:1738-1748. 10.1093/pcp/pci009, 15653793.
    • (2004) Plant Cell Physiol , vol.45 , pp. 1738-1748
    • Nanjo, T.1    Futamura, N.2    Nishiguchi, M.3    Igasaki, T.4    Shinozaki, K.5    Shinohara, K.6
  • 17
    • 33746913459 scopus 로고    scopus 로고
    • Analysis of 70,000 EST sequences to study divergence between two closely related Populus species
    • Unneberg P, Stromberg M, Lundeberg J, Jansson S, Sterky F. Analysis of 70,000 EST sequences to study divergence between two closely related Populus species. Tree Genet Genomes 2005, 1:109-115.
    • (2005) Tree Genet Genomes , vol.1 , pp. 109-115
    • Unneberg, P.1    Stromberg, M.2    Lundeberg, J.3    Jansson, S.4    Sterky, F.5
  • 18
    • 1342267353 scopus 로고    scopus 로고
    • Microsatellites for use in Nothofagus cunninghamii (Nothofagaceae) and related species
    • Jones RC, Vaillancourt RE, Jordan GJ. Microsatellites for use in Nothofagus cunninghamii (Nothofagaceae) and related species. Mol Ecol Notes 2004, 4(1):14-16.
    • (2004) Mol Ecol Notes , vol.4 , Issue.1 , pp. 14-16
    • Jones, R.C.1    Vaillancourt, R.E.2    Jordan, G.J.3
  • 19
    • 20044390277 scopus 로고    scopus 로고
    • SSR markers for analyzing South American Nothofagus species
    • Azpilicueta M, Caron H, Bodénès C, Gallo L. SSR markers for analyzing South American Nothofagus species. Silvae Genet 2004, 53:240-243.
    • (2004) Silvae Genet , vol.53 , pp. 240-243
    • Azpilicueta, M.1    Caron, H.2    Bodénès, C.3    Gallo, L.4
  • 20
    • 46449130952 scopus 로고    scopus 로고
    • A new set of highly polymorphic nuclear microsatellite markers for Nothofagus nervosa and related South American species
    • Marchelli P, Caron H, Azpilicueta M, Gallo L. A new set of highly polymorphic nuclear microsatellite markers for Nothofagus nervosa and related South American species. Silvae Genet 2008, 57(2):82-85.
    • (2008) Silvae Genet , vol.57 , Issue.2 , pp. 82-85
    • Marchelli, P.1    Caron, H.2    Azpilicueta, M.3    Gallo, L.4
  • 21
    • 78651291452 scopus 로고    scopus 로고
    • Development of novel genomic microsatellite markers in the southern beech Nothofagus pumilio (Poepp. et Endl.) Krasser
    • Soliani C, Sebastiani F, Marchelli P, Gallo L, Vendramin GG. Development of novel genomic microsatellite markers in the southern beech Nothofagus pumilio (Poepp. et Endl.) Krasser. Mol Ecol, Resources 2010, 10:404-408.
    • (2010) Mol Ecol, Resources , vol.10 , pp. 404-408
    • Soliani, C.1    Sebastiani, F.2    Marchelli, P.3    Gallo, L.4    Vendramin, G.G.5
  • 24
    • 77951894310 scopus 로고    scopus 로고
    • Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    • 10.1186/1471-2164-11-180, 2851599, 20233449
    • Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 2010, 11:180. 10.1186/1471-2164-11-180, 2851599, 20233449.
    • (2010) BMC Genomics , vol.11 , pp. 180
    • Parchman, T.L.1    Geist, K.S.2    Grahnen, J.A.3    Benkman, C.W.4    Buerkle, C.A.5
  • 25
    • 79952501970 scopus 로고    scopus 로고
    • Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels
    • 10.1186/1471-2164-12-148, 3061936, 21401935
    • Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J. Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 2011, 12:148. 10.1186/1471-2164-12-148, 3061936, 21401935.
    • (2011) BMC Genomics , vol.12 , pp. 148
    • Rismani-Yazdi, H.1    Haznedaroglu, B.Z.2    Bibby, K.3    Peccia, J.4
  • 27
    • 0027399530 scopus 로고
    • Identification of protein coding regions by database similarity search
    • 10.1038/ng0393-266, 8485583
    • Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet 1993, 3(3):266-272. 10.1038/ng0393-266, 8485583.
    • (1993) Nat Genet , vol.3 , Issue.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 28
    • 24644503098 scopus 로고    scopus 로고
    • BLAST2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    • 10.1093/bioinformatics/bti610, 16081474
    • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. BLAST2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676. 10.1093/bioinformatics/bti610, 16081474.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Götz, S.2    García-Gómez, J.M.3    Terol, J.4    Talón, M.5    Robles, M.6
  • 32
    • 67649085779 scopus 로고    scopus 로고
    • Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection
    • 10.1186/1471-2229-9-51, 2688492, 19426529
    • Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology 2009, 9:51. 10.1186/1471-2229-9-51, 2688492, 19426529.
    • (2009) BMC Plant Biology , vol.9 , pp. 51
    • Barakat, A.1    DiLoreto, D.S.2    Zhang, Y.3    Smith, C.4    Baier, K.5    Powell, W.A.6    Wheeler, N.7    Sederoff, R.8    Carlson, J.E.9
  • 34
    • 78651337304 scopus 로고    scopus 로고
    • De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)
    • 10.1186/1471-2164-12-30, 3027159, 21232141
    • Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 2011, 12:30. 10.1186/1471-2164-12-30, 3027159, 21232141.
    • (2011) BMC Genomics , vol.12 , pp. 30
    • Logacheva, M.D.1    Kasianov, A.S.2    Vinogradov, D.V.3    Samigullin, T.H.4    Gelfand, M.S.5    Makeev, V.J.6    Penin, A.A.7
  • 36
    • 0028952245 scopus 로고
    • Simple repetitive DNA sequences from primates: compilation and analysis
    • 10.1007/BF00167107, 7699718
    • Jurka J, Pethiyagoda C. Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol 1995, 40(2):120-126. 10.1007/BF00167107, 7699718.
    • (1995) J Mol Evol , vol.40 , Issue.2 , pp. 120-126
    • Jurka, J.1    Pethiyagoda, C.2
  • 37
    • 0034946803 scopus 로고    scopus 로고
    • Differential distribution of simple sequence repeats in eukaryotic genome sequences
    • 10.1093/oxfordjournals.molbev.a003903, 11420357
    • Katti MV, Ranjekar PK, Gupta VS. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 2001, 18(7):1161-1167. 10.1093/oxfordjournals.molbev.a003903, 11420357.
    • (2001) Mol Biol Evol , vol.18 , Issue.7 , pp. 1161-1167
    • Katti, M.V.1    Ranjekar, P.K.2    Gupta, V.S.3
  • 38
    • 33645754932 scopus 로고    scopus 로고
    • Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species
    • 10.1139/g05-060, 16391668
    • Kumpatla SP, Mukhopadhyay S. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 2005, 48:985-998. 10.1139/g05-060, 16391668.
    • (2005) Genome , vol.48 , pp. 985-998
    • Kumpatla, S.P.1    Mukhopadhyay, S.2
  • 39
    • 84858621000 scopus 로고    scopus 로고
    • Marcucci Poltri SN: Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
    • Acuña CV, Fernandez P, Villalba PV, García MN, Hopp HE. Marcucci Poltri SN: Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus. Tree Genet Genomes 2012, 8:289-301.
    • (2012) Tree Genet Genomes , vol.8 , pp. 289-301
    • Acuña, C.V.1    Fernandez, P.2    Villalba, P.V.3    García, M.N.4    Hopp, H.E.5
  • 41
    • 0033951367 scopus 로고    scopus 로고
    • Selection against frameshift mutations limits microsatellite expansion in coding DNA
    • 310501, 10645952
    • Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 2000, 10(1):72-80. 310501, 10645952.
    • (2000) Genome Res , vol.10 , Issue.1 , pp. 72-80
    • Metzgar, D.1    Bytof, J.2    Wills, C.3
  • 42
    • 80052825742 scopus 로고    scopus 로고
    • Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers
    • 10.1186/1471-2164-12-451, 3184296, 21929789
    • Wei W, Qi Xi Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 2011, 12:451. 10.1186/1471-2164-12-451, 3184296, 21929789.
    • (2011) BMC Genomics , vol.12 , pp. 451
    • Wei, W.1    Qi Xi Wang, L.2    Zhang, Y.3    Hua, W.4    Li, D.5    Lv, H.6    Zhang, X.7
  • 43
    • 51249169259 scopus 로고
    • A simple and efficient method for isolating RNA from pines trees
    • Chang S, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pines trees. Plant Mol Biol Rep 1993, 11(2):113-116.
    • (1993) Plant Mol Biol Rep , vol.11 , Issue.2 , pp. 113-116
    • Chang, S.1    Puryear, J.2    Cairney, J.3
  • 44
    • 0033990048 scopus 로고    scopus 로고
    • Primer 3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky HJ. Primer 3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132(3):365-386.
    • (2000) Methods Mol Biol , vol.132 , Issue.3 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.J.2
  • 45
    • 33750831582 scopus 로고    scopus 로고
    • Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
    • 10.1186/1471-2105-7-474, 1634758, 17064419
    • Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 2006, 7:474. 10.1186/1471-2105-7-474, 1634758, 17064419.
    • (2006) BMC Bioinformatics , vol.7 , pp. 474
    • Kohany, O.1    Gentles, A.J.2    Hankus, L.3    Jurka, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.