메뉴 건너뛰기




Volumn 10, Issue 7, 2015, Pages

De novo assembly and annotation of the Chinese chive (Allium tuberosum Rottler ex Spr.) transcriptome using the Illumina platform

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA; TRANSCRIPTOME;

EID: 84941771402     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0133312     Document Type: Article
Times cited : (27)

References (27)
  • 1
    • 0012706719 scopus 로고    scopus 로고
    • Sulphur compounds in alliums in relation to flavour quality
    • Rabinowitch H, Currah L, editors, Oxford: CABI Publishing
    • Randle WM, Lancaster JE. Sulphur compounds in alliums in relation to flavour quality. In: Rabinowitch H, Currah L, editors. Allium Crop science-recent advances. Oxford: CABI Publishing; 2002. pp. 1-62.
    • (2002) Allium Crop Science-recent Advances , pp. 1-62
    • Randle, W.M.1    Lancaster, J.E.2
  • 3
    • 84910014551 scopus 로고    scopus 로고
    • RNA-Seq analysis and de novo transcriptome assembly of Jerusalem artichoke (helianthus tuberosus Linne)
    • 25375764
    • Jung WY, Lee SS, Kim CW, Kim HS, Min SR, Moon JS, et al. RNA-Seq analysis and de novo transcriptome assembly of Jerusalem artichoke (helianthus tuberosus Linne). PLOS ONE. 2014;9:e111982. doi: 10.1371/journal.pone.0111982 PMID: 25375764
    • (2014) PLOS ONE. , vol.9 , pp. e111982
    • Jung, W.Y.1    Lee, S.S.2    Kim, C.W.3    Kim, H.S.4    Min, S.R.5    Moon, J.S.6
  • 4
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • 21191423
    • Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011;12:87-98. doi: 10.1038/nrg2934 PMID: 21191423
    • (2011) Nat Rev Genet. , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 5
    • 84857219324 scopus 로고    scopus 로고
    • Next-generation sequencing technologies for gene expression profiling in plants
    • 22155524
    • Jain M. Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics. 2012;11:63-70. doi: 10.1093/bfgp/elr038 PMID: 22155524
    • (2012) Brief Funct Genomics. , vol.11 , pp. 63-70
    • Jain, M.1
  • 6
    • 84893360798 scopus 로고    scopus 로고
    • De novo assembly and characterization of Sophora Japonica transcriptome using RNA-seq
    • Zhu L, Zhang Y, Guo W, Xu XJ, Wang Q. De novo assembly and characterization of Sophora Japonica transcriptome using RNA-seq. BioMed Res Int. 2014; article ID: 750961.
    • (2014) BioMed Res Int.
    • Zhu, L.1    Zhang, Y.2    Guo, W.3    Xu, X.J.4    Wang, Q.5
  • 7
    • 67650915750 scopus 로고    scopus 로고
    • Shedding light on an extremophile lifestyle through transcriptomics
    • 19549131
    • Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. Shedding light on an extremophile lifestyle through transcriptomics. New Phytol. 2009;183:764-775. doi: 10.1111/j.1469-8137.2009.02913.x PMID: 19549131
    • (2009) New Phytol. , vol.183 , pp. 764-775
    • Dassanayake, M.1    Haas, J.S.2    Bohnert, H.J.3    Cheeseman, J.M.4
  • 8
    • 84898013232 scopus 로고    scopus 로고
    • De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification
    • 24626227
    • Zhou Y, Chen L, Fan X, Bian Y. De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification. PLOS ONE. 2014;9:e91740. doi: 10. 1371/journal.pone.0091740 PMID: 24626227
    • (2014) PLOS ONE. , vol.9 , pp. e91740
    • Zhou, Y.1    Chen, L.2    Fan, X.3    Bian, Y.4
  • 9
    • 84863393816 scopus 로고    scopus 로고
    • Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
    • 22186186
    • Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, et al. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2012;99:193-208. doi: 10.3732/ajb.1100394 PMID: 22186186
    • (2012) Am J Bot. , vol.99 , pp. 193-208
    • Zalapa, J.E.1    Cuevas, H.2    Zhu, H.3    Steffan, S.4    Senalik, D.5    Zeldin, E.6
  • 10
    • 84897098475 scopus 로고    scopus 로고
    • Transcriptome sequencing and de novo analysis of Youngia japonica using the Illumina platform
    • 24595283
    • Peng Y, Gao X, Li R, Cao G. Transcriptome sequencing and de novo analysis of Youngia japonica using the Illumina platform. PLOS ONE. 2014;9:e90636. doi: 10.1371/journal.pone.0090636 PMID: 24595283
    • (2014) PLOS ONE. , vol.9 , pp. e90636
    • Peng, Y.1    Gao, X.2    Li, R.3    Cao, G.4
  • 11
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • 21572440
    • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644-652. doi: 10. 1038/nbt.1883 PMID: 21572440
    • (2011) Nat Biotechnol. , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3    Levin, J.Z.4    Thompson, D.A.5    Amit, I.6
  • 12
    • 84866436067 scopus 로고    scopus 로고
    • De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing
    • 22684307
    • Sun X, Zhou S, Meng F, Liu S. De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep. 2012;31:1823-1828. doi: 10.1007/s00299-012-1295-z PMID: 22684307
    • (2012) Plant Cell Rep. , vol.31 , pp. 1823-1828
    • Sun, X.1    Zhou, S.2    Meng, F.3    Liu, S.4
  • 13
    • 84921930784 scopus 로고    scopus 로고
    • Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)
    • Tsukazaki H, Yaguchi S, Husei Sato S, Hirakawa H, Katayose Y, Kanamori H, et al. Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum). Mol Breeding. 2015;35:55.
    • (2015) Mol Breeding. , vol.35 , pp. 55
    • Tsukazaki, H.1    Yaguchi, S.2    Husei Sato, S.3    Hirakawa, H.4    Katayose, Y.5    Kanamori, H.6
  • 14
    • 84941764124 scopus 로고    scopus 로고
    • Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)
    • Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, et al. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.). DNA Res, 2014; dsu035.
    • (2014) DNA Res , pp. dsu035
    • Kim, S.1    Kim, M.S.2    Kim, Y.M.3    Yeom, S.I.4    Cheong, K.5    Kim, K.T.6
  • 15
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • 16081474
    • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics. 2005;21:3674-3676. PMID: 16081474
    • (2005) Bioinformatics. , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 17
    • 84888428694 scopus 로고    scopus 로고
    • Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq
    • Guo H, Ye CX, Wang AL, Xian JA, Liao SA, Miao YT, et al. Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq. Fish Shellfish Immun. 2013;35:2008-2016.
    • (2013) Fish Shellfish Immun. , vol.35 , pp. 2008-2016
    • Guo, H.1    Ye, C.X.2    Wang, A.L.3    Xian, J.A.4    Liao, S.A.5    Miao, Y.T.6
  • 18
    • 84883039263 scopus 로고    scopus 로고
    • De novo transcriptome assembly of drought tolerant CAM plants, agave deserti and agave tequilana
    • 23957668
    • Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A. De novo transcriptome assembly of drought tolerant CAM plants, agave deserti and agave tequilana. BMC Genomics. 2013;14:563. doi: 10.1186/1471-2164-14-563 PMID: 23957668
    • (2013) BMC Genomics. , vol.14 , pp. 563
    • Gross, S.M.1    Martin, J.A.2    Simpson, J.3    Abraham-Juarez, M.J.4    Wang, Z.5    Visel, A.6
  • 19
    • 84912567166 scopus 로고    scopus 로고
    • RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion
    • 25415343
    • Liu Q, Wen C, Zhao H, Zhang L, Wang J, Wang Y. RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion. PLOS ONE. 2014;9:e113290. doi: 10.1371/journal.pone.0113290 PMID: 25415343
    • (2014) PLOS ONE. , vol.9 , pp. e113290
    • Liu, Q.1    Wen, C.2    Zhao, H.3    Zhang, L.4    Wang, J.5    Wang, Y.6
  • 20
    • 84899789860 scopus 로고    scopus 로고
    • High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis
    • 24682075
    • Kim HA, Lim CJ, Kim S, Choe JK, Jo SH, Baek N, et al. High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis. PLOS One 2014;9(3):e92087. doi: 10.1371/journal.pone.0092087 PMID: 24682075
    • (2014) PLOS One , vol.9 , Issue.3 , pp. e92087
    • Kim, H.A.1    Lim, C.J.2    Kim, S.3    Choe, J.K.4    Jo, S.H.5    Baek, N.6
  • 21
    • 84924288534 scopus 로고    scopus 로고
    • Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
    • 25609311
    • Kamenetsky R, Faigenboim A, Mayer ES, Michael TB, Gershberg C, Kimhi S, et al. Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.). BMC Genomics, 2015;16:12. doi: 10.1186/s12864-015-1212-2 PMID: 25609311
    • (2015) BMC Genomics , vol.16 , pp. 12
    • Kamenetsky, R.1    Faigenboim, A.2    Mayer, E.S.3    Michael, T.B.4    Gershberg, C.5    Kimhi, S.6
  • 22
    • 84906959616 scopus 로고    scopus 로고
    • De novo assembly and characterization of the fruit Transcriptome of Chinese jujube (Ziziphus jujuba Mill.) using 454 Pyrosequencing and the development of novel tri-nucleotide SSR Markers
    • 25184704
    • Li Y, Xu C, Lin X, Cui B, Wu R, Pang X. De novo assembly and characterization of the fruit Transcriptome of Chinese jujube (Ziziphus jujuba Mill.) using 454 Pyrosequencing and the development of novel tri-nucleotide SSR Markers. PLOS ONE. 2014;9:e106438. doi: 10.1371/journal.pone.0106438 PMID: 25184704
    • (2014) PLOS ONE. , vol.9 , pp. e106438
    • Li, Y.1    Xu, C.2    Lin, X.3    Cui, B.4    Wu, R.5    Pang, X.6
  • 23
    • 84876057339 scopus 로고    scopus 로고
    • De novo sequence assembly and characterization of Lycoris aurea transcriptome using GS FLX titanium platform of 454 pyrosequencing
    • 23593220
    • Wang R, Xu S, Jiang Y, Jiang J, Li X, Liang L, et al. De novo sequence assembly and characterization of Lycoris aurea transcriptome using GS FLX titanium platform of 454 pyrosequencing. PLOS ONE. 2013;8:e60449. doi: 10.1371/journal.pone.0060449 PMID: 23593220
    • (2013) PLOS ONE. , vol.8 , pp. e60449
    • Wang, R.1    Xu, S.2    Jiang, Y.3    Jiang, J.4    Li, X.5    Liang, L.6
  • 24
    • 84861170775 scopus 로고    scopus 로고
    • De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree. (Hevea brasiliensis Muell. Arg.)
    • Li D, Deng Z, Qin B, Liu X, Men Z. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree. (Hevea brasiliensis Muell. Arg.). BMC Genomics 2012;13(1):192.
    • (2012) BMC Genomics , vol.13 , Issue.1 , pp. 192
    • Li, D.1    Deng, Z.2    Qin, B.3    Liu, X.4    Men, Z.5
  • 26
    • 84869171930 scopus 로고    scopus 로고
    • Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa
    • 23167289
    • Shahin A, Van Kaauwen M, Esselink D, Bargsten JW, Van Tuyl JM, Visser RG, et al. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa. BMC Genomics. 2012;13:640. doi: 10.1186/1471-2164-13-640 PMID: 23167289
    • (2012) BMC Genomics. , vol.13 , pp. 640
    • Shahin, A.1    Van Kaauwen, M.2    Esselink, D.3    Bargsten, J.W.4    Van Tuyl, J.M.5    Visser, R.G.6
  • 27
    • 84941774953 scopus 로고    scopus 로고
    • De novo assembled transcriptome analysis and SSR marker development of a mixture of six tissues from Lilium Oriental hybrid 'Sorbonne'
    • Du F, Wu Y, Zhang L, Li XW, Zhao XY, Wang WH, et al. De novo assembled transcriptome analysis and SSR marker development of a mixture of six tissues from Lilium Oriental hybrid 'Sorbonne'. Plant Mol Biol Rep. 2014:1-13.
    • Plant Mol Biol Rep. , vol.2014 , pp. 1-13
    • Du, F.1    Wu, Y.2    Zhang, L.3    Li, X.W.4    Zhao, X.Y.5    Wang, W.H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.