메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Draft genome sequence of the rubber tree Hevea brasiliensis

(29)  Rahman, Ahmad Yamin Abdul a   Usharraj, Abhilash O a   Misra, Biswapriya B a   Thottathil, Gincy P a   Jayasekaran, Kandakumar a   Feng, Yun b   Hou, Shaobin c   Ong, Su Yean a   Ng, Fui Ling a   Lee, Ling Sze a   Tan, Hock Siew a   Sakaff, Muhd Khairul Luqman Muhd a   Teh, Beng Soon a   Khoo, Bee F a   Badai, Siti Suriawati a   Aziz, Nurohaida Ab a   Yuryev, Anton d   Knudsen, Bjarne e   Dionne Laporte, Alexandre c,h   Mchunu, Nokuthula P f   more..


Author keywords

Euphorbiaceae; Genome; Hevea brasiliensis; Natural rubber

Indexed keywords

CAROTENOID; F BOX PROTEIN; PHYTOHORMONE; REPETITIVE DNA; TRANSCRIPTION FACTOR; ALLERGEN; LATEX; RUBBER;

EID: 84873030734     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-75     Document Type: Article
Times cited : (206)

References (90)
  • 2
    • 0034053392 scopus 로고    scopus 로고
    • Alternative sources of natural rubber
    • 10.1007/s002530051627, 10803889
    • Mooibroek H, Cornish K. Alternative sources of natural rubber. Appl Microbiol Biotechnol 2000, 53:355-365. 10.1007/s002530051627, 10803889.
    • (2000) Appl Microbiol Biotechnol , vol.53 , pp. 355-365
    • Mooibroek, H.1    Cornish, K.2
  • 3
    • 34248160512 scopus 로고    scopus 로고
    • Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments
    • 10.1263/jbb.103.287, 17502267
    • Sakdapipanich JT. Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments. J Biosci Bioeng 2007, 103:287-292. 10.1263/jbb.103.287, 17502267.
    • (2007) J Biosci Bioeng , vol.103 , pp. 287-292
    • Sakdapipanich, J.T.1
  • 4
    • 0345256451 scopus 로고    scopus 로고
    • Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis: a key factor participating in natural rubber biosynthesis
    • 10.1046/j.1432-1033.2003.03863.x, 14622254
    • Asawatreratanakul K, Zhang YW, Wititsuwannakul D, Wititsuwannakul R, Takahashi S, Rattanapittayaporn A, Koyama T. Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis: a key factor participating in natural rubber biosynthesis. Eur J Biochem 2003, 270:4671-4680. 10.1046/j.1432-1033.2003.03863.x, 14622254.
    • (2003) Eur J Biochem , vol.270 , pp. 4671-4680
    • Asawatreratanakul, K.1    Zhang, Y.W.2    Wititsuwannakul, D.3    Wititsuwannakul, R.4    Takahashi, S.5    Rattanapittayaporn, A.6    Koyama, T.7
  • 5
    • 84874020717 scopus 로고    scopus 로고
    • Natural rubber biosynthesis and physic-chemical studies on plant derived latex
    • Croatia: Intech Open Acess Publisher, Elnashar M
    • Gronover CS, Wahler D, Prüfer D. Natural rubber biosynthesis and physic-chemical studies on plant derived latex. Biotechnology of Biopolymers 2011, 75-88. Croatia: Intech Open Acess Publisher, Elnashar M.
    • (2011) Biotechnology of Biopolymers , pp. 75-88
    • Gronover, C.S.1    Wahler, D.2    Prüfer, D.3
  • 7
    • 80052611733 scopus 로고    scopus 로고
    • RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis
    • 10.1007/s11103-011-9811-z, 21811850
    • Xia Z, Xu H, Zhai J, Li D, Luo H, He C, Huang X. RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 2011, 77:299-308. 10.1007/s11103-011-9811-z, 21811850.
    • (2011) Plant Mol Biol , vol.77 , pp. 299-308
    • Xia, Z.1    Xu, H.2    Zhai, J.3    Li, D.4    Luo, H.5    He, C.6    Huang, X.7
  • 9
    • 84861872022 scopus 로고    scopus 로고
    • Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets
    • 10.1186/1471-2229-12-18, 3368772, 22330773
    • Gébelin V, Argout X, Engchuan W, Pitollat B, Duan C, Montoro P, Leclercq J. Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. BMC Plant Biol 2012, 12:18. 10.1186/1471-2229-12-18, 3368772, 22330773.
    • (2012) BMC Plant Biol , vol.12 , pp. 18
    • Gébelin, V.1    Argout, X.2    Engchuan, W.3    Pitollat, B.4    Duan, C.5    Montoro, P.6    Leclercq, J.7
  • 10
    • 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.)
    • 10.1186/1471-2164-13-192, 3431226, 22607098
    • 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, 13:192. 10.1186/1471-2164-13-192, 3431226, 22607098.
    • (2012) BMC Genomics , vol.13 , pp. 192
    • Li, D.1    Deng, Z.2    Qin, B.3    Liu, X.4    Men, Z.5
  • 11
    • 84864352611 scopus 로고    scopus 로고
    • Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing
    • 10.1007/s00425-012-1622-1, 22407387
    • Lertpanyasampatha M, Gao L, Kongsawadworakul P, Viboonjun U, Chrestin H, Liu R, Chen X, Narangajavana J. Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing. Planta 2012, 236:437-445. 10.1007/s00425-012-1622-1, 22407387.
    • (2012) Planta , vol.236 , pp. 437-445
    • Lertpanyasampatha, M.1    Gao, L.2    Kongsawadworakul, P.3    Viboonjun, U.4    Chrestin, H.5    Liu, R.6    Chen, X.7    Narangajavana, J.8
  • 13
    • 0031718558 scopus 로고    scopus 로고
    • Molecular cytogenetic studies in rubber, Hevea brasiliensis Muell. Arg. (Euphorbiaceae)
    • Leitch AR, Lim KY, Leitch IJ, O'Neill M, Chye ML, Low FC. Molecular cytogenetic studies in rubber, Hevea brasiliensis Muell. Arg. (Euphorbiaceae). Genome 1998, 41:464-467.
    • (1998) Genome , vol.41 , pp. 464-467
    • Leitch, A.R.1    Lim, K.Y.2    Leitch, I.J.3    O'Neill, M.4    Chye, M.L.5    Low, F.C.6
  • 14
    • 0030850119 scopus 로고    scopus 로고
    • Nuclear DNA amounts in angiosperms-583 new estimates
    • Bennett MD, Leitch IJ. Nuclear DNA amounts in angiosperms-583 new estimates. Ann Bot 1997, 80:169-196.
    • (1997) Ann Bot , vol.80 , pp. 169-196
    • Bennett, M.D.1    Leitch, I.J.2
  • 16
    • 83155191799 scopus 로고    scopus 로고
    • Plantagora: modeling whole genome sequencing and assembly of plant genomes.
    • 10.1371/journal.pone.0028436, 3236183, 22174807
    • Barthelson R, McFarlin AJ, Rounsley SD, Young S. Plantagora: modeling whole genome sequencing and assembly of plant genomes. PLoS One 2011, 6:e28436. 10.1371/journal.pone.0028436, 3236183, 22174807.
    • (2011) PLoS One , vol.6
    • Barthelson, R.1    McFarlin, A.J.2    Rounsley, S.D.3    Young, S.4
  • 20
    • 84870265846 scopus 로고    scopus 로고
    • A physical, genetic and functional sequence assembly of the barley genome
    • The International Barley Genome Sequencing Consortium
    • The International Barley Genome Sequencing Consortium A physical, genetic and functional sequence assembly of the barley genome. Nature 2012, 491:711-716. The International Barley Genome Sequencing Consortium.
    • (2012) Nature , vol.491 , pp. 711-716
  • 22
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
    • 10.1186/gb-2008-9-1-r7, 2395244, 18190707
    • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 2008, 9:R7. 10.1186/gb-2008-9-1-r7, 2395244, 18190707.
    • (2008) Genome Biol , vol.9
    • Haas, B.J.1    Salzberg, S.L.2    Zhu, W.3    Pertea, M.4    Allen, J.E.5    Orvis, J.6    White, O.7    Buell, C.R.8    Wortman, J.R.9
  • 24
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan - an integration platform for the signature-recognition methods in InterPro
    • 10.1093/bioinformatics/17.9.847, 11590104
    • Zdobnov EM, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 25
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • 10.1093/nar/gkh063, 308797, 14681412
    • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 10.1093/nar/gkh063, 308797, 14681412.
    • (2004) Nucleic Acids Res , vol.32
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3    Okuno, Y.4    Hattori, M.5
  • 28
    • 79952702685 scopus 로고    scopus 로고
    • Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships
    • 10.1016/j.gene.2011.01.002, 21241787
    • Tangphatsornruang S, Uthaipaisanwong P, Sangsrakru D, Chanprasert J, Yoocha T, Jomchai N, Tragoonrung S. Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene 2011, 475:104-112. 10.1016/j.gene.2011.01.002, 21241787.
    • (2011) Gene , vol.475 , pp. 104-112
    • Tangphatsornruang, S.1    Uthaipaisanwong, P.2    Sangsrakru, D.3    Chanprasert, J.4    Yoocha, T.5    Jomchai, N.6    Tragoonrung, S.7
  • 32
    • 77956440518 scopus 로고    scopus 로고
    • The sucrose transporter HbSUT3 plays an active role in sucrose loading to laticifer and rubber productivity in exploited trees of Hevea brasiliensis (para rubber tree)
    • 10.1111/j.1365-3040.2010.02175.x, 20492551
    • Tang C, Huang D, Yang J, Liu S, Sakr S, Li H, Zhou Y, Qin Y. The sucrose transporter HbSUT3 plays an active role in sucrose loading to laticifer and rubber productivity in exploited trees of Hevea brasiliensis (para rubber tree). Plant Cell Environ 2010, 33:1708-1720. 10.1111/j.1365-3040.2010.02175.x, 20492551.
    • (2010) Plant Cell Environ , vol.33 , pp. 1708-1720
    • Tang, C.1    Huang, D.2    Yang, J.3    Liu, S.4    Sakr, S.5    Li, H.6    Zhou, Y.7    Qin, Y.8
  • 33
    • 85051983825 scopus 로고
    • The formation of isoprenoids in Hevea latex
    • Boca Raton: CRC Press, d'Auzac J, Jacob JL, Chrestin L
    • Kekwick RGO. The formation of isoprenoids in Hevea latex. Physiology of Rubber Tree Latex 1989, 145-164. Boca Raton: CRC Press, d'Auzac J, Jacob JL, Chrestin L.
    • (1989) Physiology of Rubber Tree Latex , pp. 145-164
    • Kekwick, R.G.O.1
  • 34
    • 1542685246 scopus 로고    scopus 로고
    • Transcriptome analysis reveals novel features of the molecular events occurring in the laticifers of Hevea brasiliensis (para rubber tree)
    • Ko JH, Chow KS, Han KH. Transcriptome analysis reveals novel features of the molecular events occurring in the laticifers of Hevea brasiliensis (para rubber tree). Plant Mol Biol 2003, 53:479-492.
    • (2003) Plant Mol Biol , vol.53 , pp. 479-492
    • Ko, J.H.1    Chow, K.S.2    Han, K.H.3
  • 36
    • 9644283093 scopus 로고    scopus 로고
    • Significant role of bacterial undecaprenyl diphosphate (C55-UPP) for rubber synthesis by Hevea latex enzymes
    • 10.1002/mabi.200400096, 15543542
    • Rattanapittayaporn A, Wititsuwannakul D, Wititsuwannakul R. Significant role of bacterial undecaprenyl diphosphate (C55-UPP) for rubber synthesis by Hevea latex enzymes. Macromol Biosci 2004, 4:1039-1052. 10.1002/mabi.200400096, 15543542.
    • (2004) Macromol Biosci , vol.4 , pp. 1039-1052
    • Rattanapittayaporn, A.1    Wititsuwannakul, D.2    Wititsuwannakul, R.3
  • 37
    • 0037322820 scopus 로고    scopus 로고
    • Molecular analysis of cis-prenyl chain elongating enzymes
    • 10.1039/b108934j, 12636086
    • Kharel Y, Koyama T. Molecular analysis of cis-prenyl chain elongating enzymes. Nat Prod Rep 2003, 20:111-118. 10.1039/b108934j, 12636086.
    • (2003) Nat Prod Rep , vol.20 , pp. 111-118
    • Kharel, Y.1    Koyama, T.2
  • 38
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • 10.1093/molbev/msr121, 3203626, 21546353
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 39
    • 78751613558 scopus 로고    scopus 로고
    • Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata
    • 10.1534/genetics.110.116582, 2927771, 20498299
    • Dillon SK, Nolan M, Li W, Bell C, Wu HX, Southerton SG. Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata. Genetics 2010, 185:1477-1487. 10.1534/genetics.110.116582, 2927771, 20498299.
    • (2010) Genetics , vol.185 , pp. 1477-1487
    • Dillon, S.K.1    Nolan, M.2    Li, W.3    Bell, C.4    Wu, H.X.5    Southerton, S.G.6
  • 40
    • 0033792207 scopus 로고    scopus 로고
    • The cellulose synthase superfamily
    • 10.1104/pp.124.2.495, 1539280, 11027699
    • Richmond TA, Somerville CR. The cellulose synthase superfamily. Plant Physiol 2000, 124:495-498. 10.1104/pp.124.2.495, 1539280, 11027699.
    • (2000) Plant Physiol , vol.124 , pp. 495-498
    • Richmond, T.A.1    Somerville, C.R.2
  • 41
    • 22444446783 scopus 로고    scopus 로고
    • The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
    • 10.1007/s00425-005-1498-4, 15940463
    • Djerbi S, Lindskog M, Arvestad L, Sterky F, Teeri TT. The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes. Planta 2005, 221:739-746. 10.1007/s00425-005-1498-4, 15940463.
    • (2005) Planta , vol.221 , pp. 739-746
    • Djerbi, S.1    Lindskog, M.2    Arvestad, L.3    Sterky, F.4    Teeri, T.T.5
  • 43
    • 4744349055 scopus 로고    scopus 로고
    • Systemic acquired resistance
    • 10.1146/annurev.phyto.42.040803.140421, 15283665
    • Durrant WE, Dong X. Systemic acquired resistance. Annu Rev Phytopathol 2004, 42:185-209. 10.1146/annurev.phyto.42.040803.140421, 15283665.
    • (2004) Annu Rev Phytopathol , vol.42 , pp. 185-209
    • Durrant, W.E.1    Dong, X.2
  • 44
    • 71349087912 scopus 로고    scopus 로고
    • Genome-wide identification of NBS-encoding resistance genes in Brassica rapa
    • 10.1007/s00438-009-0492-0, 2777221, 19838736
    • Mun JH, Yu HJ, Park S, Park BS. Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Genet Genomics 2009, 282:617-631. 10.1007/s00438-009-0492-0, 2777221, 19838736.
    • (2009) Mol Genet Genomics , vol.282 , pp. 617-631
    • Mun, J.H.1    Yu, H.J.2    Park, S.3    Park, B.S.4
  • 45
    • 0035988431 scopus 로고    scopus 로고
    • Allergenic protein of natural rubber latex
    • 10.1016/S1046-2023(02)00049-X, 12079415
    • Yeang HY, Arif SAM, Yusof F, Sunderasan E. Allergenic protein of natural rubber latex. Methods 2002, 27:32-45. 10.1016/S1046-2023(02)00049-X, 12079415.
    • (2002) Methods , vol.27 , pp. 32-45
    • Yeang, H.Y.1    Arif, S.A.M.2    Yusof, F.3    Sunderasan, E.4
  • 46
    • 0037076266 scopus 로고    scopus 로고
    • Systemic wound signaling in plants: a new perception
    • 10.1073/pnas.112196499, 124432, 12011413
    • Ryan CA, Moura DS. Systemic wound signaling in plants: a new perception. Proc Natl Acad Sci USA 2002, 99:6519-6520. 10.1073/pnas.112196499, 124432, 12011413.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6519-6520
    • Ryan, C.A.1    Moura, D.S.2
  • 47
    • 79953254420 scopus 로고    scopus 로고
    • Evolutionary and comparative analysis of MYB and bHLH plant transcription factors.
    • Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J 2011, 6:94-116.
    • (2011) Plant J , vol.6 , pp. 94-116
    • Feller, A.1    Machemer, K.2    Braun, E.L.3    Grotewold, E.4
  • 48
    • 40549134512 scopus 로고    scopus 로고
    • Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice
    • 10.1186/1471-2164-9-44, 2267713, 18221561
    • Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics 2008, 9:44. 10.1186/1471-2164-9-44, 2267713, 18221561.
    • (2008) BMC Genomics , vol.9 , pp. 44
    • Wang, D.1    Guo, Y.2    Wu, C.3    Yang, G.4    Li, Y.5    Zheng, C.6
  • 49
    • 51449111835 scopus 로고    scopus 로고
    • Green transcription factors: a Chlamydomonas overview
    • 10.1534/genetics.107.086090, 2390610, 18493038
    • Riaño-Pachón DM, Corrêa LGG, Trejos-Espinosa R, Mueller-Roeber B. Green transcription factors: a Chlamydomonas overview. Genetics 2008, 179:31-39. 10.1534/genetics.107.086090, 2390610, 18493038.
    • (2008) Genetics , vol.179 , pp. 31-39
    • Riaño-Pachón, D.M.1    Corrêa, L.G.G.2    Trejos-Espinosa, R.3    Mueller-Roeber, B.4
  • 50
    • 77953286060 scopus 로고    scopus 로고
    • WRKY transcription factors
    • 10.1016/j.tplants.2010.02.006, 20304701
    • Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci 2010, 15:247-258. 10.1016/j.tplants.2010.02.006, 20304701.
    • (2010) Trends Plant Sci , vol.15 , pp. 247-258
    • Rushton, P.J.1    Somssich, I.E.2    Ringler, P.3    Shen, Q.J.4
  • 51
    • 34547982039 scopus 로고    scopus 로고
    • MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress
    • 10.1186/1471-2164-8-242, 1947970, 17640358
    • Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 2007, 8:242. 10.1186/1471-2164-8-242, 1947970, 17640358.
    • (2007) BMC Genomics , vol.8 , pp. 242
    • Arora, R.1    Agarwal, P.2    Ray, S.3    Singh, A.K.4    Singh, V.P.5    Tyagi, A.K.6    Kapoor, S.7
  • 53
    • 27744566733 scopus 로고    scopus 로고
    • Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development
    • 10.1387/ijdb.041968pm, 16096959
    • Más P. Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development. Int J Dev Biol 2005, 49:491-500. 10.1387/ijdb.041968pm, 16096959.
    • (2005) Int J Dev Biol , vol.49 , pp. 491-500
    • Más, P.1
  • 54
    • 34249819663 scopus 로고    scopus 로고
    • F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress
    • 10.1104/pp.106.091900, 1851844, 17293439
    • Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 2007, 143:1467-1483. 10.1104/pp.106.091900, 1851844, 17293439.
    • (2007) Plant Physiol , vol.143 , pp. 1467-1483
    • Jain, M.1    Nijhawan, A.2    Arora, R.3    Agarwal, P.4    Ray, S.5    Sharma, P.6    Kapoor, S.7    Tyagi, A.K.8    Khurana, J.P.9
  • 55
    • 57749114494 scopus 로고    scopus 로고
    • The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants
    • 10.1104/pp.108.121921, 2577272, 18775973
    • Yang X, Kalluri UC, Jawdy S, Gunter LE, Yin T, Tschaplinski TJ, Weston DJ, Ranjan P, Tuskan GA. The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. Plant Physiol 2008, 148:1189-1200. 10.1104/pp.108.121921, 2577272, 18775973.
    • (2008) Plant Physiol , vol.148 , pp. 1189-1200
    • Yang, X.1    Kalluri, U.C.2    Jawdy, S.3    Gunter, L.E.4    Yin, T.5    Tschaplinski, T.J.6    Weston, D.J.7    Ranjan, P.8    Tuskan, G.A.9
  • 56
    • 79551550373 scopus 로고    scopus 로고
    • Phylogenetic comparison of F-box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift
    • 10.1371/journal.pone.0016219, 3030570, 21297981
    • Hua Z, Zou C, Shiu SH, Vierstra RD. Phylogenetic comparison of F-box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS One 2011, 6:e16219. 10.1371/journal.pone.0016219, 3030570, 21297981.
    • (2011) PLoS One , vol.6
    • Hua, Z.1    Zou, C.2    Shiu, S.H.3    Vierstra, R.D.4
  • 57
    • 75649097452 scopus 로고    scopus 로고
    • Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis
    • 10.1007/s00438-009-0495-x, 19890663
    • Chaudhary N, Nijhawan A, Khurana JP, Khurana P. Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis. Mol Genet Genomics 2010, 283:13-33. 10.1007/s00438-009-0495-x, 19890663.
    • (2010) Mol Genet Genomics , vol.283 , pp. 13-33
    • Chaudhary, N.1    Nijhawan, A.2    Khurana, J.P.3    Khurana, P.4
  • 59
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • 10.1016/j.ygeno.2010.03.001, 2874646, 20211242
    • Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95:315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 60
    • 84860584906 scopus 로고    scopus 로고
    • RepeatModeler http://www.repeatmasker.org/RepeatModeler.html.
    • RepeatModeler
  • 62
    • 84870661434 scopus 로고    scopus 로고
    • RepeatMasker http://www.repeatmasker.org.
    • RepeatMasker
  • 64
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 65
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 67
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • 10.1186/1471-2105-6-31, 553969, 15713233
    • Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. 10.1186/1471-2105-6-31, 553969, 15713233.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 69
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    • 10.1093/bioinformatics/bti310, 15728110
    • Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875. 10.1093/bioinformatics/bti310, 15728110.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 70
    • 0031573382 scopus 로고    scopus 로고
    • A tool for analyzing and annotating genomic sequences
    • 10.1006/geno.1997.4984, 9403056
    • Huang X, Adams MD, Zhou H, Kerlavage AR. A tool for analyzing and annotating genomic sequences. Genomics 1997, 46:37-45. 10.1006/geno.1997.4984, 9403056.
    • (1997) Genomics , vol.46 , pp. 37-45
    • Huang, X.1    Adams, M.D.2    Zhou, H.3    Kerlavage, A.R.4
  • 71
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • 187518, 11932250
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 72
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • 10.1101/gr.10.4.516, 310882, 10779491
    • Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10:516-522. 10.1101/gr.10.4.516, 310882, 10779491.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 73
    • 23144444421 scopus 로고    scopus 로고
    • AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
    • 10.1093/nar/gki458, 1160219, 15980513
    • Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res 2005, 33:W465-W467. 10.1093/nar/gki458, 1160219, 15980513.
    • (2005) Nucleic Acids Res , vol.33
    • Stanke, M.1    Morgenstern, B.2
  • 74
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    • 10.1093/bioinformatics/bth315, 15145805
    • Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 2004, 20:2878-2879. 10.1093/bioinformatics/bth315, 15145805.
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 75
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • 10.1186/1471-2105-5-59, 421630, 15144565
    • Korf I. Gene finding in novel genomes. BMC Bioinformatics 2004, 5:59. 10.1186/1471-2105-5-59, 421630, 15144565.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 76
    • 57149099395 scopus 로고    scopus 로고
    • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • 10.1101/gr.081612.108, 2593577, 18757608
    • Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 2008, 18:1979-1990. 10.1101/gr.081612.108, 2593577, 18757608.
    • (2008) Genome Res , vol.18 , pp. 1979-1990
    • Ter-Hovhannisyan, V.1    Lomsadze, A.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 77
    • 33846880338 scopus 로고    scopus 로고
    • Using geneid to identify genes
    • New York: John Wiley and Sons Inc, Baxevanis AD, Davison DB, Unit 4.3
    • Blanco E, Parra G, Guigó R. Using geneid to identify genes. Current Protocols in Bioinformatics 2002, New York: John Wiley and Sons Inc, Baxevanis AD, Davison DB, Unit 4.3.
    • (2002) Current Protocols in Bioinformatics
    • Blanco, E.1    Parra, G.2    Guigó, R.3
  • 82
    • 84862221167 scopus 로고    scopus 로고
    • SMART 7: recent updates to the protein domain annotation resource
    • Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 2012, 40:D303-D305.
    • (2012) Nucleic Acids Res , vol.40
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 83
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • 146525, 9023104
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 146525, 9023104.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 84
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 85
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • 10.1038/nmeth.1701, 21959131
    • Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786. 10.1038/nmeth.1701, 21959131.
    • (2011) Nat Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 86
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • 10.1126/science.252.5009.1162, 17797907
    • Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science 1991, 252:1162-1164. 10.1126/science.252.5009.1162, 17797907.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 87
    • 2642654227 scopus 로고    scopus 로고
    • MPW: the metabolic pathways database
    • 10.1093/nar/26.1.43, 147231, 9407141
    • Selkov E, Grechkin Y, Mikhailova N, Selkov E. MPW: the metabolic pathways database. Nucleic Acids Res 1998, 26:43-45. 10.1093/nar/26.1.43, 147231, 9407141.
    • (1998) Nucleic Acids Res , vol.26 , pp. 43-45
    • Selkov, E.1    Grechkin, Y.2    Mikhailova, N.3    Selkov, E.4
  • 88
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • 10.1101/gr.1224503, 403725, 12952885
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 89
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • 10.1093/sysbio/syq010, 20525638
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321. 10.1093/sysbio/syq010, 20525638.
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 90
    • 84874017963 scopus 로고    scopus 로고
    • Rubber Genome Browser http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/.
    • Rubber Genome Browser


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.