Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD)

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Liu, Jin Ping ^a   Xia, Zhi Qiang ^b   Tian, Xiao Yan ^a   Li, Yi Jian ^b  

^a HAINAN UNIVERSITY   (China)

^b INSTITUTE OF TROPICAL BIOSCIENCE AND BIOTECHNOLOGY   (China)

Author keywords

Jasmonate synthesis; Latex biosynthesis; Rubber tree; TPD; Transcriptome

Indexed keywords

ISOPENTENYL DIPHOSPHATE; JASMONIC ACID; LATEX; RUBBER; TRANSCRIPTOME; CYCLOPENTANE DERIVATIVE; MESSENGER RNA; OXYLIPIN; PLANT PROTEIN; PLANT RNA;

ARTICLE; BIOINFORMATICS; BIOSYNTHESIS; COMPARATIVE GENE MAPPING; CONTIG MAPPING; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; GENE EXPRESSION PROFILING; GENE EXPRESSION SYSTEM; GENE FUNCTION; GENE IDENTIFICATION; GENE LIBRARY; GENE ONTOLOGY; GENETIC ASSOCIATION; GENETIC DATABASE; HEVEA BRASILIENSIS; NONHUMAN; PLANT PARAMETERS; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; TAPPING PANEL DRYNESS; TRANSCRIPTION REGULATION; GENE EXPRESSION REGULATION; GENETICS; HEVEA; METABOLISM; PLANT DISEASE; PROCEDURES;

HEVEA BRASILIENSIS;

CYCLOPENTANES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HEVEA; OXYLIPINS; PLANT DISEASES; PLANT PROTEINS; RNA, MESSENGER; RNA, PLANT; RUBBER; SEQUENCE ANALYSIS, RNA;

EID: 84929401848     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1562-9     Document Type: Article

References (84)

1. Priyadarshan PM, Gonçalves PS, Omokhafe KO. Breeding Hevea rubber. In: Jain SM, Priyadarshan PM, editor. In Breeding plantation tree crops: tropical species. New York: Springer; 2009. p. 469-522.
2. Mooibroek H, Cornish K. Alternative sources of natural rubber. Appl Microbiol Biotechnol. 2000;53:355-65.
3. Chen S-C, Peng S-Q, Huang G-X, Wu K, Fu X, Chen Z. Association of decreased expression of a Myb transcription factor with the TPD (tapping panel dryness) syndrome in Hevea brasiliensis. Plant Mol Biol. 2002;51:51-8.
4. Li D-J, Deng Z, Chen C-L, Xia Z-H, Wu M, He P, et al. Identification and characterization of genes associated with tapping panel dryness from Hevea brasiliensis latex using suppression subtractive hybridization. BMC Plant Biol. 2010;10:140.
5. Taysum HH: Yield increase by the treatment of Hevea brasiliensis with antibiotics. Proceedings of the RRIM Planters' Conference: 19-21 July 1960; Kuala Lumpur 1960:132-138.
6. Zheng GB, Chen MR. Study of the cause for brown blast disease. Chin J Trop Crops. 1982;3:57-61.
7. Soyza AG. The investigation of the occurring rule and distributing pattern of brown blast disease of rubber tree in Sri Lanka. J Rubber Res Inst Sri Lanka. 1983;61:1-6.
8. Li ZY. The relationship of brown blast of rubber trees and over exploitation. Chin J Trop Agri. 1982;5:12-6.
9. Wang CZ. The report about bark of TPD Hevea brasiliansis inoculating. Chin J Trop Agri. 1988;11:25-30.
10. Nandris D, Chrestin H, Noirot M, Nicole M, Thouvenel JC, Geiger JP. The phloem necrosis of the trunk of rubber tree in Ivory Coast. (1) Symptomatology and biochemical characteristics. Eur J For Path. 1991;21:325-39.
11. Nandris D, Thouvenel JC, Nicole M, Chrestin H, Rio B, Noirot M. The phloem necrosis of the trunk of the rubber tree in Ivory Coast. (2) Etiology of the disease. Eur J For Path. 1991;21:340-53.
12. Chrestin H. iochemical aspects of bark dryness induced by overstimulation of rubber trees with ethrel. In: D'Auzac J, Jacob JL, Chrestin H, editors. In Physiology of Rubber Tree Latex. Florida, USA: Boca Raton: CRC Press; 1989. p. 431-42.
13. de Fay E, Jacob JL. Symptomatological, histological and cytological aspects. In: D'Auzac J, Jacob JL, Chrestin H, editors. In Physiology of Rubber Tree Latex. Boca Raton: CRC Press; 1989. p. 407-28.
14. Fan SW, Yang SQ. Cause of disease and hypothesis on tapping panel dryness of Hevea brasiliensis. Chin J of Trop Crops Res. 1984;18:43-8.
15. Jacob JL, Prevot JC, Laccrotte R. Tapping panel dryness in Hevea brasiliensis. Plantations, Recherche, Développement. 1994;2:15-21.
16. Faridah Y, Siti Arija MA, Ghandimathi H. Changes in some physiological latex parameters in relation to over exploitation and onset of induced tapping panel dryness. J Nat Rubber Res. 1996;10:182-6.
17. Tupy J, Primot L. Control of carbohydrate metabolism by ethylene in latex vessels in Hevea brasiliensis in relation to rubber production. Biol Plant. 1976;18:373-84.
18. Pakianathan SW, Samsidar H, Sivakumaran S, Gomez JB. Physiological and anatomical investigation on long term ethephon-stimulated trees. J Rubber Res Inst Malaysia. 1982;30:63-79.
19. Sivakumaran S, Pakianathan S-W, Abraham PD. Continuous yield stimulation. Plausible cause of yield decline. J Rubber Res Inst Malaysia. 1984;32:119-43.
20. Tupy J. Nucleic acid in latex and production of rubber in Hevea brasiliensis. J Rubber Res Inst Malaysia. 1969;21:468-76.
21. Fan SW, Yang SQ. Tapping panel dryness induced by excessive tapping is a local senescence phenomenon. Chin J Trop Crops Res. 1995;19:15-22.
22. Zeng RZ. The relation between contents of nucleic acid and tapping panel dryness in latex from Hevea brasiliensis. Chin J Crops. 1997;18:10-5.
23. Fan XW, Yang SQ. Cause of disease and hypothesis on tapping panel dryness of Hevea brasiliensis. China J Trop Crops Res. 1994;18:43-8.
24. Xi WX, Xiao XZ. Study on peroxidase isozyme and syperoxyde dismutase isozyme of TPD hevea trees. Chin J Trop Crops. 1988;9:31-6.
25. Krishnakumar R, Cornish K, Jacob J. Rubber biosynthesis in tapping panel dryness affected Hevea trees. J Nat Rubber Res. 2001;4:131-9.
26. Chrestin H, Bangratz J, d'Auzac J, Jacob JL. Role of the lutoidic tonoplast in the senescence and degeneration of the laticifers of Hevea brasiliensis. Z Pflanzenphysiol. 1984;114:261.
27. Sookmark U, Pujade-Renaud V, Chrestin H, Lacotem R, Naiyanetr C, Seguin M, et al. Characterization of polypeptides accumulated in the latex cytosol of rubber trees affected by the tapping panel dryness syndrome. Plant Cell Physiol. 2002;43:1323-33.
28. Darussamin A, Suharyanto S, Chaidamsari T. Change in the chemical composition and electrophoretic profile of latex and bark protein related to tapping panel dryness incidence in Hevea brasiliensis. Menara Perkebunan. 1995;63:52-9.
29. Dian K, Sangare A, Diopoh JK. Evidence for specific variations of protein pattern during tapping panel dryness condition development in Hevea brasiliensis. Plant Sci. 1995;105:207-16.
30. Lacrotte R, Gidrol X, Vichitcholchai N, Pujade-Renaud V, Narangajavana J, Chrestin H. Protein markers of tapping panel dryness. Plant Rech Dev. 1995;2:40-5.
31. Venkatachalam P, Thulaseedharan A, Raghothama K. Molecular identification and characterization of a gene associated with the onset of tapping paneldryness (TPD) syndrome in rubber tree (Hevea brasiliensis Muell.) by mRNA differential display. Mol Biotechnol. 2009;41((1):42-52.
32. Venkatachalam P, Geetha N, Priya P, Thulaseedharan A. Identification of a differentially expressed thymidine kinase gene related to tapping panel dryness syndrome in the rubber tree (Hevea brasiliensis Muell.Arg.) by random amplified polymorphic DNA screening. INT J Plant Biol. 2010;1(1):e7.
33. Venkatachalam P, Thulaseedharan A, Raghothama K. Identification of expression profiles of tapping panel dryness (TPD) associated genes from the latex of rubber tree (Hevea brasiliensis Muell. Arg.). Planta. 2007;226(2):499-515.
34. Qin B, Liu X-H, Deng Z, Li D-J. Identification of genes associated with tapping panel dryness in Hevea brasiliensis using oligonucleotide microarrays. Chin J Trop Crops. 2012;33(2):296-301.
35. Schuster SC. Next-generation sequencing transforms today's biology. Nat Methods. 2008;5(1):16-8.
36. Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H. Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics. 2008;92:187-94.
37. Ansorge WJ. Next-generation DNA sequencing techniques. N Biotechnol. 2009;25(4):195-203.
38. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63.
39. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet. 2010;11:31-46.
40. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011;12:87-98.
41. Van Verk MC, Hickman R, Pieterse CMJ, Van Wees SCM. RNA-Seq: revelation of the messengers. Trends Plant Sci. 2013;18:175-9.
42. Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb). 2011;107:1-15.
43. Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and interlab portability over five microarray platforms. Nucleic Acids Res. 2008;36:e141.
44. Xiang LX, He D, Dong WR, Zhang YW, Shao JZ. Deep sequencing based transcriptome profiling analysis of bacteria-challenged lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics. 2010;11:472.
45. Tang Q, Ma XJ, Mo CM, Wilson IW, Song C, Zhao H, et al. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNAseq and digital gene expression analysis. BMC Genomics. 2011;12:343.
46. Xia Z, Xu H, Zhai J, Li D, Luo H, He C, et al. RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol. 2011;77:299-308.
47. Pootakham W, Chanprasert J, Jomchai N, Sangsrakru D, Yoocha T, Therawattanasuk K, et al. Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae). Am J Bot. 2011;98:e337-8.
48. Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, et al. Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res. 2011;18:471-82.
49. 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.
50. Chow K-S, Mat-Isa MN, Bahari A, Ghazali A-K, Alias H, Mohd-Zainuddin Z, et al. Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot. 2012;63:1863-71.
51. Duan C, Argout X, Gébelin V, Summo M, Dufayard JF, Leclercq J, et al. Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing. BMC Genomics. 2013;14:30.
52. Rahman AY, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, Feng Y, et al. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics. 2013;14:75.
53. Gronover CS, Wahler D, Prüfer D. Natural rubber biosynthesis and physicchemical studies on plant derived latex. In: Elnashar M, editor. In Biotechnology of Biopolymers. Croatia: Intech Open Acess Publishe; 2011. p. 75--88.
54. Cornish K. Biochemistry of natural rubber, a vital raw material, emphasizing biosynthetic rate, molecular weight and compartmentalization, in evolutionarily divergent plant species. Nat Prod Rep. 2001;18:182-9.
55. da Costa BMT, Keasling JD, McMahan CM, Cornish K. Magnesium ion regulation of in vitro rubber biosynthesis by Parthenium argentatum Gray. Phytochemistry. 2006;67:1621-8.
56. Okada K. The biosynthesis of isoprenoids and the mechanisms regulating it in plants. Biosci Biotechnol Biochem. 2011;75(7):1219-25.
57. Sando T, Takaoka C, Mukai Y, Yamashita A, Hattori M. Cloning and characterization of mevalonate pathway genes in natural rubber producing plant. Hevea brasiliensis Biosci Biotechnol Biochem. 2008;72(8):2049-60.
58. Sando T, Takeno S, Watanabe N, Okumoto H. 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(11):2903-17.
59. Brown MS, Goldstein JL. Multivalent feedback regulation of HMG CoA reductase, a control mechanism coordinating isoprenoid synthesis and cell growth. J Lipid Res. 1980;21:505-17.
60. Chang W-C, Song H, Liu H-W, Liu P-H. Current development in isoprenoid precursor biosynthesis and regulation. Curr Opin Chem Biol. 2013;17(4):571-9.
61. Krishnakumar R, Sreelatha S, Thomas M, Gopalakrishnan J, Jacob J, Sethuraj MR. Biochemical composition of soft bark tissues in Hevea affected by tapping panel dryness. Indian J Nat Rubber Res. 1999;12(1,2):92-9.
62. Krishnakumar R, Annamalainathan K, Simon SP, Jacob J. Tapping panel dryness syndrome in Hevea increases dark respiration but not ATP status. Indian J Nat Rubber Res. 2001;14(1):14-9.
63. Chrestin H, Jacob JL, D'Auzac J. Biochemical basis for cessation of latex flow and occurrence of physiological bark dryness. Kuala Lumpur, Malaysia: Proceedings of the International Rubber Conference. 1985;1985(3):20-42.
64. Siswanto. Physiological mechanism related to latex production of Hevea brasiliensis. Buletin-Bioteknologi-Perkebunan. 1994;1(1):23-9.
65. Sethuraj MR. Present status of investigations in the Rubber Research Institute of India on panel dryness syndrome, Proceeding of the IRRDB Workshop on Tree Dryness, 26-27 June 1989. Penang, Malaysia; 1989. p. 37-40.
66. Kombrink E. Chemical and genetic exploration of jasmonate biosynthesis and signaling paths. Planta. 2012;236:1351-66.
67. Suwanmanee P, Sirinupong N, Suvachittanont W: Regulation of 3-hydroxy-3-methylglutaryl-CoA synthase and 3-hydroxy-3-methylglutaryl-CoA reductase and rubber biosynthesis of Hevea brasiliensis (B.H.K.) Mull. Arg. In Isoprenoid Synthesis in Plants and Microorganisms: New Concepts and Experimental Approaches. Edited by Bach TJ, Rohmer M. Berlin/Heidelberg/New York: Springer-Verlag; 2013:315-28.
68. Burnett RJ, Maldonado-Mendoza IE, McKnight TD, Nessler CL. Expression of a 3-hydroxy-3-methylglutaryl coenzyme a reductase gene from Camptotheca acuminate: Is differentially regulated by wounding and methyl Jasmonate. Plant Physiol. 1993;103:41-8.
69. Mehrjerdi MZ, Bihamta M-R. Omidi M, a Naghavi M-R, Soltanloo H, Ranjbar M: Effects of exogenous methyl jasmonate and 2-isopentenyladenine on artemisinin production and gene expression in Artemisia annua. Turk J Bot. 2013;37:499-505.
70. Choi D, Bostock RM, Avdiushko S, Hildebrand DF. Lipid-derived signals that discriminate wound- and pathogen-responsive isoprenoid pathways in plants: methyl jasmonate and the fungal elicitor arachidonic acid induce different 3-hydroxy-3-methylglutaryl-coenzyme A reductase genes and antimicrobial isoprenoids in Solanum tuberosum L. Proc Natl Acad Sci U S A. 1994;91(6):2329-33.
71. Hao BZ, Wu JL. Laticifer differentiation in Hevea brasiliensis: induction by exogenous jasmonic acid and linolenic acid. Ann Bot. 2000;85(1):37-43.
72. Shi M-J, Tian W-M. Effect on the induction of the secondary laticifer differentiation by the transportation of exogenous JA in Hevea brasiliensis. Chin J Trop Crops. 2012;33(9):1647-53.
73. Zhang L, Xing D. Methyl jasmonate induces production of reactive oxygen species and alterations in mitochondrial dynamics that precede photosynthetic dysfunction and subsequent cell death. Plant Cell Physiol. 2008;49:1092-111.
74. Vanková R. Plant hormone functions in abiotic and biotic stress responses. In: Pessarakli M, editor. In Handbook of Plant and Crop Stress, 3rd Edition. Boca Raton, Florida: CRC Press; 2010. p. 191-211.
75. Das G, Raj S, Pothen J, Sethuraj MR, Sinha TP, Sen-Mandi S. Status of free radical and its scavenging system with stimulation in Hevea brasiliensis. Plant Physio Biochem. 1998;25(1):47-50.
76. Grabherr MG, Haas BJ, Levin JZ, Thompson DA, Amit I, Adiconis X, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech. 2011;29(7):644-52.
77. Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999;138-48.
78. 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. Bioinforma. 2005;21(18):3674-6.
79. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34(Web Server issue):W293-7.
80. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36(Database issue):D480-4.
81. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621-8.
82. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res. 1997;7(10):986-95.
83. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001;29:1165-88.
84. Li X-Y, Sun H-Y, Pei J-B, Dong Y-Y, Wang F-W, Chen H, et al. De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants. Gene. 2012;511:54-61.