Abstract
Trans-polyisoprene rubber is produced in the tissues of leaves, bark, and fruit of Eucommia ulmoides and is considered an important energy source. Transcript profiles of two tissues from E. ulmoides cv. Qinzhong No. 3, leaf and fruit, were analysed using the Illumina HiSeq 2000 system. In total, 104 million clean reads were obtained and assembled into 58,863 unigenes. Through gene functional classification, 28,091 unigenes (47.72%) were annotated and 65 unigenes have been hypothesized to encode proteins involved in terpenoid biosynthesis. In addition, 10,041 unigenes were detected as differentially expressed unigenes, and 29 of them were putatively related to terpenoid biosynthesis. The synthesis of trans-polyisoprene rubbers in E. ulmoides was hypothesised to be dominated by the mevalonate pathway. Farnesyl diphosphate synthase 2 (FPPS2) was considered a key component in the biosynthesis of trans-polyprenyl diphosphate. Rubber elongation factor 3 (REF3) might be involved in stabilising the membrane of rubber particles in E. ulmoides. To date, 351 simple sequence repeats (SSRs) were validated as polymorphisms from eight E. ulmoides plants (two parent plants and six F1 individuals), and these could act as molecular markers for genetic map density increase and breeding improvement of E. ulmoides.
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References
Du H, Xie B, Shao S (2003) Prospects and research progress of gutta-percha. J Cent South For Univ 23(4):96–99
Hu SY (1979) A contribution to our knowledge of Tu-chung: Eucommia ulmoides. Am J Chin Med 7(1):5–37. https://doi.org/10.1142/s0192415x79000039
Sih CJ, Ravikumar PR, Huang FC, Buckner C (1976) Isolation and synthesis of pinoresinol diglucoside, a major antihypertensive principle of Tu-Chung (Eucommia ulmoides, Oliver). J Am Chem Soc 98(17):5412–5413
Kawasaki T, Uezono K, Nakazawa Y (2000) Antihypertensive mechanism of food for specified health use: “Eucommia leaf glycoside” and its clinical application. J Health Sci 22:29–36
Chen LJ, Hu TW, Huang LC (1995) A protocol toward multiplication of the medicinal tree, Eucommia ulmoides Oliver. In Vitro Cell Dev Biol Plant 31(4):193–198
Guo T, Liu Y, Wei Y, Ma X, Fan Q, Ni J, Yin Z, Liu J, Wang S, Dong Y, Zhang J, Zhang L, Su H, Tan T (2015) Simultaneous qualitation and quantitation of natural trans-1,4-polyisoprene from Eucommia ulmoides Oliver by gel permeation chromatography (GPC). J Chromatogr B 1004:17–22. https://doi.org/10.1016/j.jchromb.2015.09.007
Chen R, Namimatsu S, Nakadozono Y, Bamba T, Nakazawa Y, Gyokusen K (2008) Efficient regeneration of Eucommia ulmoides from hypocotyl explant. Biol Plant 52(4):713–717. https://doi.org/10.1007/s10535-008-0137-x
Zhiqiang S, Fangdong L, Hongyan D, Jingle Z (2013) A novel silvicultural model for increasing biopolymer production from Eucommia ulmoides Oliver trees. Ind Crops Prod 42(1):216–222
Bamba T, Fukusaki E, Nakazawa Y, Kobayashi A (2002) In-situ chemical analyses of trans-polyisoprene by histochemical staining and Fourier transform infrared microspectroscopy in a rubber-producing plant, Eucommia ulmoides Oliver. Planta 215(6):934–939. https://doi.org/10.1007/s00425-002-0832-3
Du H, Du L, Xie BX, Tana W (2006) Dynamic accumulation of gutta-percha content in Eucommia ulmoides Oliv. leaves. J Cent South For Univ 26(2):1–6
Zhang K, Ma X, Ma M, Wang L, Zhang T (1999) A study on dynamic accumulation of metabolites during the growth of Eucommia ulmoides Oliv. Sci Silvae Sin 35(2):15–20
Du H (2006) Difference of Samara’s form characters and gutta-percha content from different producing areas associated with Eucommia ulmoides. Sci Silvae Sin 42(3):35–39
Du H, Du L, Li F (2004) Dynamic of gutta-percha formation and accumulation in Samara of Eucommia ulmoides. For Res 17(2):185–191
Du H, Du L, Li F, Xie B (2004) Individual variation of gutta-percha content in samaras of Eucommia ulmoides. For Res 6:706–710
Xie B, Du H, Du L (2005) Variations of gutta-percha content in samara from different Eucommia ulmoides forms. Sci Silvae Sin 41(6):144–146
Suzuki N, Uefuji H, Nishikawa T, Mukai Y, Yamashita A, Hattori M, Ogasawara N, Bamba T, Fukusaki E-i, Kobayashi A, Ogata Y, Sakurai N, Suzuki H, Shibata D, Nakazawa Y (2012) Construction and analysis of EST libraries of the trans-polyisoprene producing plant, Eucommia ulmoides Oliver . Planta 236(5):1405–1417. https://doi.org/10.1007/s00425-012-1679-x
Yin T, Cao X, Miao Q, Li C, Chen X, Zhou M, Jiang J (2011) Molecular cloning and functional analysis of an organ-specific expressing gene coding for farnesyl diphosphate synthase from Michelia chapensis Dandy. Acta Physiol Plant 33(1):137–144. https://doi.org/10.1007/s11738-010-0529-3
Baker J, Franklin DB, Parker J (1992) Sequence and characterization of the gcpE gene of Escherichia coli. Fems Microbiol Lett 73(1–2):175
Wouters J, Oudjama Y, Ghosh S, Stalon V, Droogmans L, Oldfield E (2003) Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase. J Am Chem Soc 125(11):3198–3199
Bamba T, Murayoshi M, Gyoksen K, Nakazawa Y, Okumoto H, Katto H, Fukusaki E, Kobayashi A (2010) Contribution of mevalonate and methylerythritol phosphate pathways to polyisoprenoid biosynthesis in the rubber-producing plant Eucommia ulmoides oliver. Z Für Nat C (J Biosci) 65(5–6):363–372
Kasahara H, Hanada A, Kuzuyama T, Takagi M, Kamiya Y, Yamaguchi S (2002) Contribution of the mevalonate and methylerythritol phosphate pathways to the biosynthesis of gibberellins in Arabidopsis. J Biol Chem 277(47):45188–45194
Hemmerlin A, Hoeffler JF, Meyer O, Tritsch D, Kagan IA, Grosdemangebilliard C, Rohmer M, Bach TJ (2003) Cross-talk between the cytosolic mevalonate and the plastidial methylerythritol phosphate pathways in Tobacco bright yellow-2 cells. J Biol Chem 278(29):26666
Laule O, Fürholz A, Chang HS, Zhu T, Wang X, Heifetz PB, Gruissem W, Lange BM (2003) Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA 100(11):6866–6871
Schuhr CA, Radykewicz T, Sagner S, Latzel C, Zenk MH, Arigoni D, Bacher A, Rohdich F, Eisenreich W (2003) Quantitative assessment of crosstalk between the two isoprenoid biosynthesis pathways in plants by NMR spectroscopy. Phytochem Rev 2(1–2):3–16
Zulak KG, Bohlmann J (2010) Terpenoid biosynthesis and specialized vascular cells of conifer defense. J Integr Plant Biol 52(1):86–97
Berthelot K, Estevez Y, Deffieux A, Peruch F (2012) Isopentenyl diphosphate isomerase: a checkpoint to isoprenoid biosynthesis. Biochimie 94(8):1621–1634
Thulasiram HV, Hans K, Erickson A, Poulter CD (2008) A common mechanism for branching, cyclopropanation, and cyclobutanation reactions in the isoprenoid biosynthetic pathway. J Am Chem Soc 130(6):1966–1971
Wuyun TN, Wang L, Liu H, Wang X, Zhang L, Bennetzen JL, Li T, Yang L, Liu P, Du L (2018) The Hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesis. Mol Plant 11(3):429
Tong Z, Wang D, Sun Y, Yang Q, Meng X, Wang L, Feng W, Li L, Wurtele ES, Wang X (2017) Comparative proteomics of rubber latex revealed multiple protein species of REF/SRPP family respond diversely to ethylene stimulation among different rubber tree clones. Int J Mol Sci 18(5):958
Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). Bmc Genom.https://doi.org/10.1186/1471-2164-11-726
Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, Huang X, Han B (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-sEq. Genome Res 20(9):1238–1249. https://doi.org/10.1101/gr.106120.110
Liu H, Fu J, Du H, Hu J, Wuyun T (2016) De novo sequencing of Eucommia ulmoides flower bud transcriptomes for identification of genes related to floral development. Genom Data 9:105–110
Wang W, Zhang X (2017) Identification of the sex-biased gene expression and putative sex-associated genes in Eucommia ulmoides Oliver using comparative transcriptome analyses. Molecules 22(12):2255
Li Y, Wang D, Li Z, Wei J, Jin C, Liu M (2014) A molecular genetic linkage map of Eucommia ulmoides and Quantitative trait loci (QTL) analysis for growth traits. International Journal Of Molecular Sciences 15(2):2053–2074. https://doi.org/10.3390/ijms15022053
Dong J, Ma X, Wei Q, Peng S, Zhang S (2011) Effects of growing location on the contents of secondary metabolites in the leaves of four selected superior clones of Eucommia ulmoides. Ind Crops Prod 34(3):1607–1614
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–130. https://doi.org/10.1038/nbt.1883
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1(1):18
Rolf A, Amos B, Wu CH, Barker WC, Brigitte B, Serenella F, Elisabeth G, Hongzhan H, Rodrigo L, Michele M (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119. https://doi.org/10.1093/nar/gkh131
Minoru K, Susumu G, Shuichi K, Yasushi O, Masahiro H (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN (2003) The COG database: an updated version includes eukaryotes. Bmc Bioinform 4(1):41–41
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676. https://doi.org/10.1093/bioinformatics/bti610
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297. https://doi.org/10.1093/nar/gkl1031
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 99:138–148
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2007) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729
Bailey TL, Nadya W, Chris M, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369–W373
Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7(10):986–995
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-SEq. Nat Methods 5(7):621–628. https://doi.org/10.1038/nmeth.1226
Ye J, Jin C-F, Li N, Liu M-H, Fei Z-X, Dong L-Z, Li L, Li Z-Q (2018) Selection of suitable reference genes for qRT-PCR normalisation under different experimental conditions in Eucommia ulmoides Oliv. Sci Rep 8(1):15043. https://doi.org/10.1038/s41598-018-33342-w
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402–408
Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422. https://doi.org/10.1007/s00122-002-1031-0
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15(1):8–15. https://doi.org/10.1007/bf02772108
Zhang Q, Su Y, Zhang J (2013) Seasonal difference in antioxidant capacity and active compounds contents of Eucommia ulmoides oliver leaf. Molecules 18(2):1857–1868
Wang L, Du H, Wuyun T-n (2016) Genome-wide identification of microRNAs and their targets in the leaves and fruits of Eucommia ulmoides using high-throughput sequencing. Front Plant Sci 7:1632
Lesser MR, Parchman TL, Buerkle CA (2012) Cross-species transferability of SSR loci developed from transciptome sequencing in lodgepole pine. Mol Ecol Resour 12(3):448–455. https://doi.org/10.1111/j.1755-0998.2011.03102.x
Feng Y, Wang L, Fu J, Wuyun T, Du H, Tan X, Zou F, Li F (2016) Transcriptome sequencing discovers genes related to fatty acid biosynthesis in the seeds of Eucommia ulmoides. Genes Genom 38(3):275–283. https://doi.org/10.1007/s13258-015-0362-6
Feng Y, Zhang L, Fu J, Li F, Wang L, Tan X, Mo W, Cao H (2016) Characterization of glycolytic pathway genes using RNA-seq in developing kernels of Eucommia ulmoides. J Agric Food Chem 64(18):3712–3731. https://doi.org/10.1021/acs.jafc.5b05918
Ye J, Han W, Deng P, Jiang Y, Liu M, Li L, Li Z (2019) Comparative transcriptome analysis to identify candidate genes related to chlorogenic acid biosynthesis in Eucommia ulmoides Oliv. Trees.https://doi.org/10.1007/s00468-019-01865-y
Makita Y, Ng KK, Veera Singham G, Kawashima M, Hirakawa H, Sato S, Othman AS, Matsui M (2017) Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. DNA Res 24(2):159–167
Kajiura H, Suzuki N, Tokumoto Y, Yoshizawa T, Takeno S, Fujiyama K, Kaneko Y, Matsumura H, Nakazawa Y (2017) Two Eucommia farnesyl diphosphate synthases exhibit distinct enzymatic properties leading to end product preferences. Biochimie 139:95–106
Ohnuma S, Hirooka K, Ohto C, Nishino T (1997) Conversion from archaeal geranylgeranyl diphosphate synthase to farnesyl diphosphate synthase: two amino acids before the first aspartate-rich motif solely determine eukaryotic farnesyl diphosphate synthase activity. J Biol Chem 272(8):5192–5198. https://doi.org/10.1074/jbc.272.8.5192
Ohnuma S, Hirooka K, Tsuruoka N, Yano M, Ohto C, Nakane H, Nishino T (1998) A pathway where polyprenyl diphosphate elongates in prenyltransferase: insight into a common mechanism of chain length determination of prenyltransferases. J Biol Chem 273(41):26705–26713. https://doi.org/10.1074/jbc.273.41.26705
Okada K, Kainou T, Tanaka K, Nakagawa T, Matsuda H, Kawamukai M (1998) Molecular cloning and mutational analysis of the ddsA gene encoding decaprenyl diphosphate synthase from gluconobacter suboxydans. Eur J Biochem 255(1):52–59. https://doi.org/10.1046/j.1432-1327.1998.2550052.x
Dai LJ, Xiang QL, Yu LI, Nie ZY, Kang GJ, Duan CF, Zeng RZ (2012) Rubber particle protein analysis of Hevea brasiliensis by two dimensional 16-BAC/SDS-PAGE and mass spectrometry. Sci Agric Sin 45(11):2328–2338
Brown D, Feeney M, Ahmadi M, Lonoce C, Sajari R, Di CA, Frigerio L (2017) Subcellular localization and interactions among rubber particle proteins from Hevea brasiliensis. J Exp Bot 68(18):5045–5055
Posch A, Chen Z, Dunn MJ, Wheeler CH, Petersen A, Leubner-Metzger G, Baur X (2010) Latex allergen database. Electrophoresis 18(15):2803–2810
Hamidi MS, Gajic-Veljanoski O, Cheung AM (2003) Vitamin K and bone health. Proc Nutr Soc 62(4):839–843
Shea MK, Booth SL (2007) Role of vitamin K in the regulation of calcification. Int Congr Ser 1297(26):165–178
Nakazawa Y, Bamba T, Takeda T, Uefuji H, Harada Y, Li X, Chen R, Inoue S, Tutumi M, Shimizu T (2009) Production of Eucommia-rubber from Eucommia ulmoides Oliv. (Hardy Rubber Tree). Plant Biotechnol 26(1):71–79
Jang JC, León P, Zhou L, Sheen J (1997) Hexokinase as a sugar sensor in higher plants. Plant Cell 9(1):5–19
Li Y, Xu C, Lin X, Cui B, Wu R, Pang X (2014) De novo assembly and characterization of the fruit transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PLoS ONE 9(9):e106438
Jia H, Yang H, Sun P, Li J, Zhang J, Guo Y, Han X, Zhang G, Lu M, Hu J (2016) De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila. Sci Rep 6(1):39591. https://doi.org/10.1038/srep39591
Gang N, Lu T, Yajie Z, Linkai H, Xiao M, Xin C, Ling P, Xu Z, Xinquan Z (2017) Development of SSR markers based on transcriptome sequencing and association analysis with drought tolerance in perennial grass Miscanthus from China. Front Plant Sci 8:801. https://doi.org/10.3389/fpls.2017.00801
Yan Z, Wu F, Luo K, Zhao Y, Yan Q, Zhang Y, Wang Y, Zhang J (2017) Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research. Sci Rep 7(8):17959. doi:https://doi.org/10.1038/s41598-017-18049-8
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The work was funded by the Shaanxi Key research and development (R&D) Program (2019NY-012), Scientific Startup Foundation for Doctor of Northwest A&F University (Z109021715) and the General Financial Grant from the China Postdoctoral Science Foundation (2018M633594).
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ZL and CJ concerned and designed the research. CJ, YL, SW and ML performed the experiments. CJ conducted the work of data analysis and paper writing. CJ, ZL, LL and JY revised the paper.
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Jin, C., Li, Z., Li, Y. et al. Transcriptome analysis of terpenoid biosynthetic genes and simple sequence repeat marker screening in Eucommia ulmoides. Mol Biol Rep 47, 1979–1990 (2020). https://doi.org/10.1007/s11033-020-05294-w
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DOI: https://doi.org/10.1007/s11033-020-05294-w