Genome structure of jatropha curcas L.

Jatropha, Challenges for a New Energy Crop

Volumn 2, Issue , 2013, Pages 563-576

  Sato, Shusei ^a   Hirakawa, Hideki ^a   Tsuchimoto, Suguru ^b   Sakai, Hiroe ^b   Shibagaki, Nakako ^b   Matsunaga, Sachihiro ^b,c   Fukui, Kiichi ^b   Tabata, Satoshi ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b OSAKA UNIVERSITY   (Japan)

^c TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84929565958     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-4915-7_30     Document Type: Chapter

References (64)

1. Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y et al (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309:1052-1056
2. Achten WMJ, Verchot L, Franken YJ, Mathijs E, Singh VP, Aerts R et al (2008) Jatropha biodiesel production and use. Biomass Bioenergy 32:1063-1084
3. Alvarez-Buylla ER, Pelaz S, Liljegren SJ, Gold SE, Burgeff C, Ditta GS et al (2000) An ancestral MADS-box duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci USA 97:5328-5333
4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
5. airoch A, Apweiler R (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucl Acids Res 24:21-25
6. Carvalho CR, Clarindoa WR, Praça MM, Araújoa FS, Carels N (2008) Genome size, base composition and karyotype of Jatropha curcas L, an important biofuel plant. Plant Sci 174:613-617
7. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D et al (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 28:951-956
8. Chen MS, Wang GJ, Wang RL, Wang J, Song SQ, Xu ZF (2011) Analysis of expressed sequence tags from biodiesel plant Jatropha curcas embryos at different developmental stages. Plant Sci 181:696-700
9. Costa GG, Cardoso KC, Del Bem LE, Lima AC, Cunha MA, de Campos-Leite L et al (2010) Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L. BMC Genomics 11:462. doi:10.1186/1471-2164-11-462
10. Devappa RK, Makkar HP, Becker K (2010) Jatropha toxicity-a review. J Toxicol Environ Health B Crit Rev 13:476-507
11. Drews GN, Bowman JL, Meyerowitz EM (1991) Negative regulation of the Arabidopsis homeotic gene AGAMOUS by the APETALA2 product. Cell 65:991-1002
12. Eitas TK, Dangl JL (2010) NB-LRR proteins: pairs, pieces, perception, partners, and pathways. Curr Opin Plant Biol 13:472-477
13. Fujino K, Matsuda Y, Sekiguchi H (2009) Transcriptional activity of rice autonomous transposable element Dart. J Plant Physiol 166:1537-1543
14. Gomes KA, Almeida TC, Gesteira AS, Lôbo IP, Guimarães ACR, de Miranda AB et al (2010) ESTs from seeds to assist the selective breeding of Jatropha curcas L. for oil and active compounds. Genomics Insights 3:29-56
15. Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev 8:1548-1560
16. Gu K, Chiam H, Tian D, Yin Z (2011) Molecular cloning and expression of heteromeric ACCase subunit genes from Jatropha curcas. Plant Sci 180:642-649
17. Haas W, Sterk H, Mittelbach M (2002) Novel 12-deoxy-16-hydroxy phorbol diesters isolated from the seed oil of J. curcas. J Nat Prod 65:1434-1440
18. Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148:993-1003
19. Hartmann U, Höhmann S, Nettesheim K, Wisman E, Saedler H, Huijser P (2000) Molecular cloning of SVP: A negative regulator of the floral transition in rabidopsis. Plant J 21:351-360
20. Hirakawa H, Tsuchimoto S, Sakai H, Nakayama S, Fujishiro T, Kishida Y et al (2012) Upgraded genomic information of Jatropha curcas L. Plant Biotechnol 129:123-130
21. Huang MX, Hou P, Wei Q, Xu Y, Chen F (2008) A ribosome-inactivating protein (curcin 2) induced from Jatropha curcas can reduce viral and fungal infection in transgenic tobacco. Plant Growth Regul 54:115-123
22. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
23. Itoh Y, Hasebe M, Davies E, Takeda J, Ozeki Y (2003) Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome. Mol Genet Genomics 269:49-59
24. Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K (2002) Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev 16:2006-2020
25. Jack T, Brockman LL, Meyerowitz EM (1992) The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell 68:683-697
26. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA et al (2002) Dasheng: A recently ampli fied nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161:1293-1305
27. Joshi C, Mathur P, Khare SK (2011) Degradation of phorbol esters by Pseudomonas aeruginosa PseA during solid-state fermentation of deoiled Jatropha curcas seed cake. Bioresour Technol 102:4815-4819
28. King AJ, Li Y, Graham IA (2011) Profiling the developing Jatropha curcas L. seed transcriptome by pyrosequencing. Bioenerg Res 4:211-221
29. Kobayashi Y, Kaya H, Goto K, Iwabuchi M, Araki T (1999) A pair of related genes with antagonistic roles in mediating flowering signals. Science 286:1960-1962
30. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T et al (2002) Hd3a , a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1. under short-day conditions. Plant Cell Physiol 43:1096-1105
31. Lee JH, Yoo SJ, Park SH, Hwang I, Lee JS, Ahn JH (2007) Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev 21:397-402
32. Lee S, Choi SC, An G (2008) Rice SVP-group MADS-box proteins, OsMADS22 and OsMADS55 , are negative regulators of brassinosteroid responses. Plant J 54:93-105
33. Leseberg CH, Li A, Kang H, Duvall M, Mao L (2006) Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. Gene 378:84-94
34. Li CY, Devappa RK, Liu JX, Makkar HPS, Becker K (2010) Toxicity of Jatropha curcas phorbol esters in mice. Food Chem Toxicol 48:620-625
35. Lifschitz E, Eviatar T, Rozman A, Shalit A, Goldshmidt A, Amsellem Z et al (2006) The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proc Natl Acad Sci USA 103:6398-6403
36. Lin J, Yan F, Tang L, Chen F (2003) Antitumor effects of curcin from seeds of Jatropha curcas. Acta Pharmacol Sin 4:241-246
37. Lin Z, Zhong S, Grierson D (2009) Recent advances in ethylene research. J Exp Bot 60:3311-3336
38. Lin J, Jin YJ, Zhou X, Wang JY (2010) Molecular cloning and functional analysis of the gene encoding geranylgeranyl diphosphate synthase from J. curcas. Afr J Biotechnol 9:3342-3351
39. Luo M, Dennis ES, Berger F, Peacock WJ, Chaudhury A (2005) MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) kinase gene, are regulators of seed size in Arabidopsis. Proc Natl Acad Sci USA 102:17531-17536
40. Luo MJ, Yang XY, Liu WX, Xu Y, Huang P, Yan F et al (2006) Expression, puri fication and antitumor activity of curcin. Acta Biochim Biophys Sin 38:663-668
41. Natarajan P, Parani M (2011) De novo assembly and transcriptome analysis offive major tissues of Jatropha curcas L using GS FLX titanium platform of 454 pyrosequencing. BMC Genomics 12:191, 10.1186/1471-2164-12-191
42. Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA et al (2010) Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds. BMC Genomics 11:606. doi: 10.1186/1471-2164-11-606
43. oma K, Ohtsubo H, Ohtsubo E (2000) ATLN elements, LINEs from Arabidopsis thaliana : identification and characterization. DNA Res 7:291-303
44. Pradhan S, Naik SN, Khan MA, Sahoo P (2011) Experimental assessment of toxic phytochemicals in Jatropha curcas : oil, cake, bio-diesel and glycerol. J Sci Food Agric 92:511-519. doi:10.1002/ jsfa.4599
45. Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847-857
46. Qin W, Ming XH, Ying X, Xin SZ, Fang C (2005) Expression of a ribosome inactivating protein (curcin 2) in Jatropha curcas is induced by stress. J Biosci 30:351-357
47. Qin X, Zheng X, Shao C, Gao J, Jiang L, Zhu X (2009) Stress-induced curcin-L promoter in leaves of Jatropha curcas L. and characterization in transgenic tobacco. Planta 230:387-395
48. Saha S, Enugutti B, Rajakumari S, Rajasekharan R (2006) Cytosolic triacylglycerol biosynthetic pathway in oilseeds. Molecular cloning and expression of peanut cytosolic diacylglycerol acyltransferase. Plant Physiol 141:1533-1543
49. Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF et al (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613-1616
50. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227-239
51. Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M et al (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18:65-76
52. Stanke M, Steinkamp R, Waack S, Morgenstern B (2004) AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Res. 32(Web Server issue):W309-312
53. Stripe F, Pession-Brizzi A, Lorenzoni E, Strocchi P, Montanaro L, Sperti S (1976) Studies on the proteins from the seeds of Croton tiglium and of Jatropha curcas. Toxic properties and inhibition of protein synthesis in vitro. Biochem J 156:1-6
54. The French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467
55. Tong L, Shu MP, Wu YD, Dan WM, Ying X, Meng X et al (2006) Characterization of a new stearoyl-acyl carrier protein desaturase gene from Jatropha curcas. Biotechnol Lett 28:657-662
56. Tränkner C, Lehmann S, Hoenicka H, Hanke MV, Fladung M, Lenhardt D et al (2010) Overexpression of an FT-homologous gene of apple induces early flowering in annual and perennial plants. Planta 232:1309-1324
57. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 15:1596-1604
58. Wang BB, Brendel V (2004) The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol 5:R102
59. Wang CM, Liu P, Yi C, Gu K, Sun F, Li L et al (2011) A first generation microsatellite-and SNPbased linkage map of Jatropha. PLoS One 6(8):e23632, 10.1371/journal.pone.0023632
60. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843-859
61. Xiao J, Zhang H, Niu L, Wang X, Lu X (2011) Evaluation of detoxi fication methods on toxic and antinutritional composition and nutritional quality of proteins in Jatropha curcas meal. J Agric Food Chem 59:4040-4044
62. Yadav HK, Ranjan A, Asif MH, Mantri S, Sawant SV, Tuli R (2011) EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera. Tree Genet Genom 7:207-219
63. Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M et al (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103:19581-19586
64. Ye J, Qu J, Bui HTN, Chua NH (2009) Rapid analysis of Jatropha curcas gene functions by virusinduced gene silencing. Plant Biotechnol J 7:964-976