Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress respo

다국어 초록 (Multilingual Abstract)

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

참고문헌 (Reference)

1 Du Z, "agriGO : a GO analysis toolkit for the agricultural community" 38 : W64-W70, 2010

2 Brown RS, "Zinc finger proteins : getting a grip on RNA" 15 : 94-98, 2005

3 Liu Q, "Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain, separate two cellular signal transduction pathways in drought- and low temperature responsive gene expression, respectively, in Arabidopsis" 10 : 1391-1406, 1998

4 Liu J-P, "Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD)" 16 : 398-, 2015

5 Calzadilla PI, "Transcriptome response mediated by cold stress in Lotus japonicus" 7 : 374-, 2016

6 An D, "Transcriptome profiling of low temperature-treated Cassava apical shoots showed dynamic responses of tropical plant to cold stress" 13 : 64-, 2012

7 Jiajia Li, "Transcriptome comparative analysis between the cytoplasmic male sterile line and fertile line in soybean (Glycine max (L.) Merr.)" 한국유전학회 39 (39): 1117-1127, 2017

8 Peng Wang, "Transcriptome analysis reveals sunflower cytochrome P450 CYP93A1 responses to high salinity treatment at the seedling stage" 한국유전학회 39 (39): 581-591, 2017

9 Wenping Hua, "Transcriptome analysis of Dioscorea zingiberensis identifies genes involved in diosgenin biosynthesis" 한국유전학회 39 (39): 509-520, 2017

10 Kaplan F, "Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content" 50 : 967-981, 2007

11 Tang C, "The rubber tree genome reveals new insights into rubber production and species adaptation" 2 : 16073-, 2016

12 Song S, "The bHLH subgroup IIId factors negatively regulate jasmonate-mediated plant defense and development" 9 : e1003653-, 2013

13 Lee BH, "The Arabidopsis coldresponsive transcriptome and its regulation by ICE1" 17 : 3155-3175, 2005

14 Fernández-Calvo P, "The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses" 23 : 701-715, 2011

15 He J, "Studies on cellular injuries in rubber trees under chilling stress" 21 : 84-91, 1982

16 Lindemose S, "Structure, function and networks of transcription factors involved in abiotic stress responses" 14 : 5842-5878, 2013

17 Zhou Q-Y, "Soybean WRKY type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants" 6 : 486-503, 2008

18 Figueiredo DD, "Seven zinc-finger transcription factors are novel regulators of the stress responsive gene OsDREB1B" 63 : 3643-3656, 2012

19 Vogel JT, "Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis" 41 : 195-211, 2005

20 Solecka D, "Role of phenylpropanoid compounds in plant responses to different stress factors" 19 : 257-268, 1997

21 Park S, "Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network" 82 : 193-207, 2015

22 Wang H, "Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology" 7 : 67-, 2016

23 Matthews L, "Reactome knowledgebase of human biological pathways and processes" 37 : D619-D622, 2009

24 Croft D, "Reactome : a database of reactions, pathways and biological processes" 39 : D691-D697, 2011

25 Pushparajah E, "Problems and potentials for establishing Hevea under difficult environmental conditions" 59 : 242-251, 1983

26 Petrussa E, "Plant flavonoids—biosynthesis, transport and involvement in stress responses" 14 : 14950-14973, 2013

27 Thomashow MF, "Plant cold acclimation freezing tolerance genes and regulatory mechanisms" 50 : 571-599, 1999

28 Lin M-X, "Physiological responses of Hevea brasiliensis during the chilling injury" 15 : 7-11, 1994

29 Wang X-J, "Physiological characteristics of Hevea brasiliensis in response to low temperature stress and its regulation mechanisms" 48 : 318-324, 2012

30 Theocharis A, "Physiological and molecular changes in plants grown at low temperatures" 235 : 1091-1105, 2012

31 Khaledian Y, "Phenylpropanoid and antioxidant changes in chickpea plants during cold stress" 62 : 772-778, 2015

32 Schaefer CF, "PID : the pathway interaction database" 37 : D674-D679, 2009

33 Thomas PD, "PANTHER : a library of protein families and subfamilies indexed by function" 13 : 2129-2141, 2003

34 Vannini C, "Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants" 37 : 115-127, 2004

35 Gilmour SJ, "Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation" 24 : 1854-1865, 2000

36 Varshney RK, "Next-generation sequencing technologies and their implications for crop genetics and breeding" 27 : 522-530, 2009

37 Huang ZD, "Natural rubber: biology, cultivation and technology" Elsevier 220-238, 1992

38 Jaradat MR, "Multiple roles of the transcription factor AtMYBR1/AtMYB44 in ABA signaling, stress responses, and leaf senescence" 13 : 192-, 2013

39 Liu J-P, "Molecular mechanism of ethylene stimulation of latex yield in rubber tree (Hevea brasiliensis). revealed by de novo sequencing and transcriptome analysis" 17 : 257-, 2016

40 Knight MR, "Low-temperature perception leading to gene expression and cold tolerance in higher plants" 195 : 737-751, 2012

41 Xie C, "KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases" 39 : W316-W322, 2011

42 Kanehisa M, "KEGG : kyoto encyclopedia of genes and genomes" 28 : 27-30, 2000

43 Sharma M, "Jasmonates : emerging players in controlling temperature stress tolerance" 6 : 1129-, 2016

44 Hu Y, "Jasmonate regulates leaf senescence and tolerance to cold stress : crosstalk with other phytohormones" 68 : 1361-1369, 2017

45 Jin J, "Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum" 18 : 496-, 2017

46 Wu ZG, "Insights from the cold transcriptome and metabolome of Dendrobium officinale : global reprogramming of metabolic and gene regulation networks during cold acclimation" 7 : 1653-, 2016

47 Christie PJ, "Impact of low-temperature stress on general phenylpropanoid and anthocyanin pathways : enhancement of transcript abundance and anthocyanin pigmentation in maize seedlings" 194 : 541-549, 1994

48 Roberts A, "Identification of novel transcripts in annotated genomes using RNA-SEq" 27 : 2325-2329, 2011

49 Eremina M, "Hormonal control of cold stress responses in plants" 73 : 797-810, 2016

50 Wang L, "Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera" 14 : 103-, 2014

51 Wei Y, "Genome-wide identification and expression analysis of the WRKY gene family in cassava" 7 : 25-, 2016

52 Chinnusamy V, "Gene regulation during cold stress acclimation in plants" 639 : 39-55, 2010

53 Provart NJ, "Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures" 132 : 893-906, 2003

54 Roy S, "Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome" 11 : e1117723-, 2016

55 Schulz E, "Flavonoids are determinants of freezing tolerance and cold acclimation in Arabidopsis thaliana" 6 : 34027-, 2016

56 Azuma A, "Flavonoid biosynthesis-related genes in grape skin are differentially regulated by temperature and light conditions" 236 : 1067-1080, 2012

57 Seo J, "Expression of the Arabidopsis AtMYB44 gene confers drought/salt-stress tolerance in transgenic soybean" 29 : 601-608, 2012

58 Karp PD, "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes" 33 : 6083-6089, 2005

59 Bahieldin A, "Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant" 16 : 216-, 2016

60 Chen B-Q, "Estimation of rubber stand age in typhoon and chilling injury afflicted area with Landsat TM data: a case study in Hainan Island, China" 274 : 222-230, 2012

61 Chalker-Scott L, "Environmental significance of anthocyanins in plant stress responses" 70 : 1-9, 1999

62 Wang Y-R, "Effects of chilling temperature of plant metabolism of Hevea brasiliensis" 20 : 44-53, 1978

63 Tian Y-H, "Effect of diurnal irradiance on night-chilling tolerance of six rubber cultivars" 54 : 374-380, 2016

64 Mai J, "Effect of chilling on photosynthesis and antioxidant enzymes in Hevea brasiliensis Muell" 23 : 863-874, 2009

65 Persak H, "Dominant repression by Arabidopsis transcription factor MYB44 causes oxidative damage and hypersensitivity to abiotic stress" 15 : 2517-2537, 2014

66 Luo P, "Differential responses of two rubber tree clones to chilling stress" 11 : 13466-13471, 2012

67 Trapnell C, "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks" 7 : 562-578, 2012

68 Trapnell C, "Differential analysis of gene regulation at transcript resolution with RNA-sEq" 31 : 46-53, 2012

69 Strickler SR, "Designing a transcriptome next generation sequencing project for a nonmodel plant species" 99 : 257-266, 2012

70 Zhan X, "De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress" 17 : 209-, 2016

71 Zhang Y, "CsWRKY46, a WRKY transcription factor from cucumber, confers cold resistance in transgenic-plant by regulating a set of cold-stress responsive genes in an ABA-dependent manner" 108 : 478-487, 2016

72 Yang QS, "Comparative transcriptomics analysis reveals difference of key gene expression between banana and plantain in response to cold stress" 16 : 446-, 2015

73 Jian Ding, "Comparative transcriptome analysis of lipid biosynthesis in seeds and non-seed tissues of sea buckthorn" 한국유전학회 39 (39): 1021-1033, 2017

74 Xicheng Wang, "Comparative transcriptome analysis of berry-sizing effects of gibberellin ( GA3) on seedless Vitis vinifera L." 한국유전학회 39 (39): 493-507, 2017

75 Chinnusamy V, "Cold stress regulation of gene expression in plants" 12 : 444-451, 2007

76 Zhao C, "Cold responsive gene transcription becomes more complex" 20 : 466-468, 2015

77 Zeng C, "Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in cassava" 14 : 207-, 2014

78 Niu Y, "Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis" 62 : 2143-2154, 2011

79 Gronover CS, "Biotechnology of biopolymers" InTech 75-88, 2011

80 Priyadarshan PM, "Biology of hevea rubber" CAB International 1-163, 2011

81 Fowler S, "Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway" 14 : 1675-1690, 2002

82 Gilmour SJ, "Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities" 54 : 767-781, 2004

83 Van Buskirk HA, "Arabidopsis transcription factors regulating cold acclimation" 126 : 72-80, 2006

84 Stockinger EJ, "Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcription activator that binds to the C repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit" 94 : 1035-1040, 1997

85 Ahmed NU, "Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa" 15 : 383-394, 2015

86 Kan L-Y, "Analysis on rubber tree cold injury in 2007/2008 winter in Hainan" 25 : 251-257, 2009

87 Mizoi J, "AP2/ERF family transcription factors in plant abiotic stress responses" 1819 : 86-96, 2012

88 Hannah MA, "A global survey of gene regulation during cold acclimation in Arabidopsis thaliana" 1 : e26-, 2005

89 Ramamoorthy R, "A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments" 49 : 865-879, 2008