Draft genome sequence of the rubber tree Hevea brasiliensis

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• 作者：Ahmad Yamin Abdul Rahman (1)
  Abhilash O Usharraj (1)
  Biswapriya B Misra (1)
  Gincy P Thottathil (1)
  Kandakumar Jayasekaran (1)
  Yun Feng (2)
  Shaobin Hou (3)
  Su Yean Ong (1)
  Fui Ling Ng (1)
  Ling Sze Lee (1)
  Hock Siew Tan (1)
  Muhd Khairul Luqman Muhd Sakaff (1)
  Beng Soon Teh (1)
  Bee Feong Khoo (1)
  Siti Suriawati Badai (1)
  Nurohaida Ab Aziz (1)
  Anton Yuryev (4)
  Bjarne Knudsen (5)
  Alexandre Dionne-Laporte (3) (9)
  Nokuthula P Mchunu (6)
  Qingyi Yu (7)
  Brennick J Langston (7)
  Tracey Allen K Freitas (10) (8)
  Aaron G Young (3)
  Rui Chen (2)
  Lei Wang (2)
  Nazalan Najimudin (1)
  Jennifer A Saito (1)
  Maqsudul Alam (1) (3) (8)
  
• 关键词：Hevea brasiliensis ; Euphorbiaceae ; Natural rubber ; Genome
• 刊名：BMC Genomics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：14
• 期：1
• 全文大小：690KB
• 参考文献：1. Prabhakaran Nair KP: / The Agronomy and Economy of Important Tree Crops of the Developing World. Burlington: Elsevier; 2010.
  2. Mooibroek H, Cornish K: Alternative sources of natural rubber. / Appl Microbiol Biotechnol 2000, 53:355鈥?65. CrossRef
  3. Sakdapipanich JT: Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments. / J Biosci Bioeng 2007, 103:287鈥?92. CrossRef
  4. 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鈥?680. CrossRef
  5. Gronover CS, Wahler D, Pr眉fer D: Natural rubber biosynthesis and physic-chemical studies on plant derived latex. In / Biotechnology of Biopolymers. Edited by: Elnashar M. Croatia: Intech Open Acess Publisher; 2011:75鈥?8.
  6. Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanprasert J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S: Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. / DNA Res 2011, 18:471鈥?82. CrossRef
  7. 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鈥?08. CrossRef
  8. Chow KS, Mat-Isa MN, Bahari A, Ghazali AK, Alias H, Mohd-Zainuddin Z, Hoh CC, Wan KL: Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. / J Exp Bot 2012, 63:1863鈥?871. CrossRef
  9. G茅belin 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. CrossRef
  10. 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. CrossRef
  11. 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鈥?45. CrossRef
  12. Pootakham W, Chanprasert J, Jomchai N, Sangsrakru D, Yoocha T, Tragoonrung S, Tangphatsornruang S: Development of genomic-derived simple sequence repeat markers in Hevea brasiliensis from 454 genome shotgun sequences. / Plant Breeding 2012, 131:555鈥?62. CrossRef
  13. Leitch AR, Lim KY, Leitch IJ, O鈥橬eill M, Chye ML, Low FC: Molecular cytogenetic studies in rubber, Hevea brasiliensis Muell. Arg. (Euphorbiaceae). / Genome 1998, 41:464鈥?67.
  14. Bennett MD, Leitch IJ: Nuclear DNA amounts in angiosperms-583 new estimates. / Ann Bot 1997, 80:169鈥?96. CrossRef
  15. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, / et al.: Genome sequencing in microfabricated high-density picolitre reactors. / Nature 2005, 437:376鈥?80.
  16. Barthelson R, McFarlin AJ, Rounsley SD, Young S: Plantagora: modeling whole genome sequencing and assembly of plant genomes. / PLoS One 2011, 6:e28436. CrossRef
  17. Le Guen V, Garcia D, Doar茅 F, Mattos CRR, Condina V, Couturier C, Chambon A, Weber C, Esp茅out S, Seguin M: A rubber tree鈥檚 durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor. / Tree Genet Genomes 2011, 7:877鈥?89. CrossRef
  18. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, / et al.: The genome of woodland strawberry (Fragaria vesca). / Nat Genet 2011, 43:109鈥?16. CrossRef
  19. van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE: The draft genome and transcriptome of Cannabis sativa. / Genome Biol 2011, 12:R102. CrossRef
  20. The International Barley Genome Sequencing Consortium: A physical, genetic and functional sequence assembly of the barley genome. / Nature 2012, 491:711鈥?16.
  21. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, / et al.: The B73 maize genome: complexity, diversity, and dynamics. / Science 2009, 326:1112鈥?115. CrossRef
  22. 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. CrossRef
  23. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A: / UniProtKB/Swiss-Prot. Methods Mol Biol. 2007, 406:89鈥?12.
  24. Zdobnov EM, Apweiler R: InterProScan - an integration platform for the signature-recognition methods in InterPro. / Bioinformatics 2001, 17:847鈥?48. CrossRef
  25. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. / Nucleic Acids Res 2004, 32:D277-D280. CrossRef
  26. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. / BMC Bioinformatics 2003, 4:41. CrossRef
  27. Finn RD, Mistry J, Schuster-B枚ckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A: Pfam: clans, web tools and services. / Nucleic Acids Res 2006, 34:D247-D251. CrossRef
  28. 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鈥?12. CrossRef
  29. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. / Nat Genet 2000, 25:25鈥?9. CrossRef
  30. Silpi U, Lacointe A, Kasempsap P, Thanysawanyangkura S, Chantuma P, Gohet E, Musigamart N, Cl茅ment A, Am茅glio T, Thaler P: Carbohydrate reserves as a competing sink: evidence from tapping rubber trees. / Tree Physiol 2007, 27:881鈥?89. CrossRef
  31. Ponciano G, McMahan CM, Xie W, Lazo GR, Coffelt TA, Collins-Silva J, Nural-Taban A, Gollery M, Shintani DK, Whalen MC: Transcriptome and gene expression analysis in cold-acclimated guayule (Parthenium argentatum) rubber-producing tissue. / Phytochemistry 2012, 79:57鈥?6. CrossRef
  32. 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鈥?720. CrossRef
  33. Kekwick RGO: The formation of isoprenoids in Hevea latex. In / Physiology of Rubber Tree Latex. Edited by: d鈥橝uzac J, Jacob JL, Chrestin L. Boca Raton: CRC Press; 1989:145鈥?64.
  34. 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鈥?92. CrossRef
  35. Sando T, Takeno S, Watanabe N, Okumoto H, Kuzuyama T, Yamashita A, Hattori M, Ogasawara N, Fukusaki E, Kobayashi A: Cloning and characterization of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway genes of a natural-rubber producing plant. / Hevea brasiliensis. Biosci Biotechnol Biochem 2008, 72:2903鈥?917. CrossRef
  36. 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鈥?052. CrossRef
  37. Kharel Y, Koyama T: Molecular analysis of cis-prenyl chain elongating enzymes. / Nat Prod Rep 2003, 20:111鈥?18. CrossRef
  38. 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鈥?739. CrossRef
  39. 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鈥?487. CrossRef
  40. Richmond TA, Somerville CR: The cellulose synthase superfamily. / Plant Physiol 2000, 124:495鈥?98. CrossRef
  41. 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鈥?46. CrossRef
  42. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, / et al.: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). / Science 2006, 313:1596鈥?604. CrossRef
  43. Durrant WE, Dong X: Systemic acquired resistance. / Annu Rev Phytopathol 2004, 42:185鈥?09. CrossRef
  44. 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鈥?31. CrossRef
  45. Yeang HY, Arif SAM, Yusof F, Sunderasan E: Allergenic protein of natural rubber latex. / Methods 2002, 27:32鈥?5. CrossRef
  46. Ryan CA, Moura DS: Systemic wound signaling in plants: a new perception. / Proc Natl Acad Sci USA 2002, 99:6519鈥?520. CrossRef
  47. Feller A, Machemer K, Braun EL, Grotewold E: Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. / Plant J 2011, 6:94鈥?16. CrossRef
  48. 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. CrossRef
  49. Ria帽o-Pach贸n DM, Corr锚a LGG, Trejos-Espinosa R, Mueller-Roeber B: Green transcription factors: a Chlamydomonas overview. / Genetics 2008, 179:31鈥?9. CrossRef
  50. Rushton PJ, Somssich IE, Ringler P, Shen QJ: WRKY transcription factors. / Trends Plant Sci 2010, 15:247鈥?58. CrossRef
  51. 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. CrossRef
  52. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, / et al.: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). / Nature 2008, 452:991鈥?96. CrossRef
  53. M谩s P: Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development. / Int J Dev Biol 2005, 49:491鈥?00. CrossRef
  54. 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鈥?483. CrossRef
  55. 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鈥?200. CrossRef
  56. 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. CrossRef
  57. 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鈥?3. CrossRef
  58. Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W: Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. / PLoS Genet 2008, 4:e3. CrossRef
  59. Miller JR, Koren S, Sutton G: Assembly algorithms for next-generation sequencing data. / Genomics 2010, 95:315鈥?27. CrossRef
  60. / RepeatModeler. http://www.repeatmasker.org/RepeatModeler.html
  61. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. / Nucleic Acids Res 2003, 31:365鈥?70. CrossRef
  62. / RepeatMasker. http://www.repeatmasker.org
  63. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. / Genome Res 2010, 20:265鈥?72. CrossRef
  64. 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. CrossRef
  65. Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. / Bioinformatics 2009, 25:1105鈥?111. CrossRef
  66. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O: Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. / Nucleic Acids Res 2003, 31:5654鈥?666. CrossRef
  67. Slater GS, Birney E: Automated generation of heuristics for biological sequence comparison. / BMC Bioinformatics 2005, 6:31. CrossRef
  68. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V: Comparative plant genomics resources at PlantGDB. / Plant Physiol 2005, 139:610鈥?18. CrossRef
  69. Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. / Bioinformatics 2005, 21:1859鈥?875. CrossRef
  70. Huang X, Adams MD, Zhou H, Kerlavage AR: A tool for analyzing and annotating genomic sequences. / Genomics 1997, 46:37鈥?5. CrossRef
  71. Kent WJ: BLAT-the BLAST-like alignment tool. / Genome Res 2002, 12:656鈥?64.
  72. Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. / Genome Res 2000, 10:516鈥?22. CrossRef
  73. 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. CrossRef
  74. Majoros WH, Pertea M, Salzberg SL: TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. / Bioinformatics 2004, 20:2878鈥?879. CrossRef
  75. Korf I: Gene finding in novel genomes. / BMC Bioinformatics 2004, 5:59. CrossRef
  76. 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鈥?990. CrossRef
  77. Blanco E, Parra G, Guig贸 R: Using geneid to identify genes. In / Current Protocols in Bioinformatics. Edited by: Baxevanis AD, Davison DB. New York: John Wiley and Sons Inc; 2002. Unit 4.3
  78. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C: The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. / Nucleic Acids Res 2011, 39:D561-D568. CrossRef
  79. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O: PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. / Nucleic Acids Res 2003, 31:334鈥?41. CrossRef
  80. Attwood TK, Mitchell AL, Gaulton A, Moulton G, Tabernero L: The PRINTS protein fingerprint database: functional and evolutionary applications. In / Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics. Edited by: Dunn M, Jorde L, Little P, Subramaniam A. New Jersey: John Wiley and Sons Ltd; 2006.
  81. Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N: PROSITE, a protein domain database for functional characterization and annotation. / Nucleic Acids Res 2010, 38:D161-D166. CrossRef
  82. Letunic I, Doerks T, Bork P: SMART 7: recent updates to the protein domain annotation resource. / Nucleic Acids Res 2012, 40:D303-D305. CrossRef
  83. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. / Nucleic Acids Res 1997, 25:955鈥?64.
  84. Altschul SF, Madden TL, Sch盲ffer 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鈥?402. CrossRef
  85. Petersen TN, Brunak S, von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. / Nat Methods 2011, 8:785鈥?86. CrossRef
  86. Lupas A, Van Dyke M, Stock J: Predicting coiled coils from protein sequences. / Science 1991, 252:1162鈥?164. CrossRef
  87. Selkov E Jr, Grechkin Y, Mikhailova N, Selkov E: MPW: the metabolic pathways database. / Nucleic Acids Res 1998, 26:43鈥?5. CrossRef
  88. Li L, Stoeckert CJ Jr, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. / Genome Res 2003, 13:2178鈥?189. CrossRef
  89. 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鈥?21. CrossRef
  90. / Rubber Genome Browser. http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/
  
• 作者单位：Ahmad Yamin Abdul Rahman (1)
  Abhilash O Usharraj (1)
  Biswapriya B Misra (1)
  Gincy P Thottathil (1)
  Kandakumar Jayasekaran (1)
  Yun Feng (2)
  Shaobin Hou (3)
  Su Yean Ong (1)
  Fui Ling Ng (1)
  Ling Sze Lee (1)
  Hock Siew Tan (1)
  Muhd Khairul Luqman Muhd Sakaff (1)
  Beng Soon Teh (1)
  Bee Feong Khoo (1)
  Siti Suriawati Badai (1)
  Nurohaida Ab Aziz (1)
  Anton Yuryev (4)
  Bjarne Knudsen (5)
  Alexandre Dionne-Laporte (3) (9)
  Nokuthula P Mchunu (6)
  Qingyi Yu (7)
  Brennick J Langston (7)
  Tracey Allen K Freitas (10) (8)
  Aaron G Young (3)
  Rui Chen (2)
  Lei Wang (2)
  Nazalan Najimudin (1)
  Jennifer A Saito (1)
  Maqsudul Alam (1) (3) (8)
  
  1. Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
  2. TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
  3. Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, USA
  4. Ariadne Genomics Inc, Rockville, Maryland, USA
  5. CLC bio, Aarhus, Denmark
  9. Centre of Excellence in Neuromics of Universit茅 de Montr茅al, Centre Hospitalier de l鈥橴niversit茅 de Montr茅al Research Center, Montr茅al, Qu茅bec, Canada
  6. Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
  7. AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University System, Weslaco, Texas, USA
  10. Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
  8. Department of Microbiology, University of Hawaii, Honolulu, Hawaii, USA
  

文摘

Background Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Results Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. Conclusions The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.