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Published December 31, 2018 | Version v1
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De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway

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  • 1. ∗ & Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India

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Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan, Tamhane, Vaijayanti A. (2018): De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway. Phytochemistry 156: 201-213, DOI: 10.1016/j.phytochem.2018.09.013, URL: http://dx.doi.org/10.1016/j.phytochem.2018.09.013

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Publication: 10.1199/tab.0144 (DOI)
Publication: 10.1155/2013/162750 (DOI)
Publication: 10.1093/molbev/msw054 (DOI)
Publication: 10.1371/journal.pone.0108719 (DOI)
Publication: 10.1038/ncomms13026 (DOI)
Publication: 10.1371/journal.pone.0136397 (DOI)
Publication: 10.3389/fpls.2015.01199 (DOI)
Publication: 10.1371/journal.pone.0129422 (DOI)
Publication: 10.1371/journal.pone.0086399 (DOI)
Publication: 10.1371/journal.pone.0160370 (DOI)
Publication: 10.1007/s10142-010-0197-9.Epub2010Oct30 (DOI)
Publication: 10.1126/sciadv.1501780 (DOI)
Publication: 10.3389/fpls.2016.00894 (DOI)
Has part
Taxonomic treatment: 10.5281/zenodo.10570085 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03881B76835D7F05FCCDE87484A2F934 (URL)
Taxonomic treatment: 10.5281/zenodo.10570087 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03881B7683587F01FCCDE8C78148FB28 (URL)
Taxonomic treatment: 10.5281/zenodo.10570089 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03881B7683597F01FF9BE8B681C6F8D9 (URL)
Taxonomic treatment: 10.5281/zenodo.10570093 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03881B7683597F01FCCDECEE8315F98B (URL)
Taxonomic treatment: 10.5281/zenodo.10570095 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03881B7683567F0FFF9BE956816CFE90 (URL)
Figure: 10.5281/zenodo.10484694 (DOI)
Dataset: http://table.plazi.org/id/DF5EFAE8835D7F05FC89EAB18477F8AA (URL)
Dataset: http://table.plazi.org/id/DF5EFAE8835E7F06FF9BECD080D5FF4B (URL)
Dataset: http://table.plazi.org/id/DF5EFAE8835E7F06FCCDECD08572FF65 (URL)
Dataset: http://table.plazi.org/id/DF5EFAE8835E7F06FF9AEA218219F9D5 (URL)
Figure: 10.5281/zenodo.10484696 (DOI)
Dataset: http://table.plazi.org/id/DF5EFAE8835F7F07FF9BE824820FFB2E (URL)
Figure: 10.5281/zenodo.10484698 (DOI)
Dataset: http://table.plazi.org/id/DF5EFAE883597F01FF86ECD08083FF4B (URL)
Figure: 10.5281/zenodo.10484700 (DOI)
Dataset: http://table.plazi.org/id/DF5EFAE8835B7F03FF72EFCA80EFF86D (URL)
Dataset: http://table.plazi.org/id/DF5EFAE883547F0CFF9BED0E8304FE07 (URL)
Figure: 10.5281/zenodo.10484702 (DOI)
Dataset: http://table.plazi.org/id/DF5EFAE883567F0EFF9BEADD8207F978 (URL)
Is source of
Dataset: https://www.gbif.org/dataset/d89294fc-5574-47eb-96ca-98b610502659 (URL)

References

  • Ahad, A., Ganai, A.A., Sareer, O., Najm, M.Z., Kausar, M.A., Mohd, M., Siddiqui, W.A., 2012. Therapeutic potential of Oroxylum indicum: a review. J. Pharmaceut. Res. Opin. 2, 163-172.
  • Ali, R.M., Houghton, P.J., Raman, A., Hoult, J.R.S., 1998. Antimicrobial and antiinflammatory activities of extracts and constituents of Oroxylum indicum (L.)Vent. Phytomedicine 5, 375-381.
  • Babu, T.H., Manjulatha, K., Kumar, G.S., Hymavathi, A., Tiwari, A.K., Purohit, M., Rao, J.M., Babu, K.S., 2010. Gastroprotective flavonoid constituents from Oroxylum indicum Vent. Bioorg. Med. Chem. Lett 20, 117-120.
  • Bak, S., Beisson, F., Bishop, G., Hamberger, B., Hofer, R., Paquette, S., Werck-Reichhart, D., 2011. Cytochromes P450, vol. 9 The Arabidopsis Book/American Society of Plant Biologists, e0144. http://doi.org/10.1199/tab.0144.
  • Bassard, J.E., Moller, L.B., Laursen, T., 2017. Assembly of dynamic P450-mediated metabolons-order versus chaos. Curr. Mol. Biol. Rep. 3, 37-51.
  • Bastos, H.P., Tavares, B., Pesquita, C., Faria, D., Couto, F.M., 2011. Application of gene ontology to gene identification. Methods Mol. Biol. 760, 141-157.
  • Bezek, S., Ujhazy, E., Mach, M., Navarova, J., Dubovicky, M., 2008. Developmental origin of chronic diseases: toxicological implication. Interdiscp. Toxicol. 1, 29-31.
  • Bomal, C., Bedon, F., Caron, S., Mansfield, S.D., Levasseur, C., Cooke, J.E., Blais, S., Tremblay, L., Morency, M.J., Pavy, N., Grima-Pettenati, J., Seguin, A., Mackay, J., 2008. Involvement of Pinus taeda MYB1and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J. Exp. Bot. 59, 3925-3939.
  • Chen, L.J., Games, D.E., Jones, J., 2003. Isolation and identification of four flavonoids constituents from the seeds of Oroxylum indicum by high-speed counter-current chromatography. J. Chromatogr. A 988, 95-105.
  • DaCheng, H., Pei, M., Jun, M., ShiLin, C., PeiGen, X., Yong, P., Li, H., LiJia, X., Chao, S., 2012. De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. China Life. Sci. 55, 452-466.
  • Dastmalchi, M., Mark, A., Bernards, M.A., Dhaubhadel, S., 2016. Twin anchors of the soybean isoflavonoid metabolon: evidence for tethering of the complex to the endoplasmic reticulum by IFS and C4H. Plant J. 85, 689-706.
  • Dao, T.T.H., Linthorst, H.J.M., Verpoorte, R., 2011. Chalcone synthase and its function in plant resistance. Phytochem. Rev. 10, 397-412.
  • Davis, G., Ananga, A., Krastanova, S., Sutton, S., Ochieng, J.W., Leong, S., Tsolova, V., 2012. Elevated gene expression in chalcone synthase enzyme suggests an increased production of flavonoids in skin and synchronized red cell cultures of North American native grape berries. DNA Cell Biol. 31, 939-945.
  • Deka, D.C., Kumar, V., Prasad, C., Kumar, K., Gogoi, B.J., Singh, L., Srivastava, R.B., 2013. Oroxylum indicum- a medicinal plant of North East India: an overview of its nutritional, remedial, and prophylactic properties. J. Appl. Pharmaceut. Sci. 3, 104-112.
  • Dinda, B., SilSarma, I., Dinda, M., Rudrapaul, P., 2015. Oroxylum indicum (L.) Kurz, an important Asian traditional medicine: from traditional uses to scientific data for its commercial exploitation. J. Ethnopharmacol. 161, 255-278.
  • El Euch, C., Jay-Allemand, C., Pastuglia, M., Doumas, P., Charpentier, J.P., Capelli, P., Jouanin, L., 1998. Expression of antisense chalcone synthase RNA in transgenic hybrid walnut microcuttings. Effect on flavonoid content and rooting ability. Plant Mol. Biol. 38, 467-479.
  • Feller, A., Machemer, K., Braun, E.L., Grotewold, E., 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66, 94-116.
  • Fujino, N., Tenma, N., Waki, T., Ito, K., Komatsuzaki, Y., Sugiyama, K., Yamazaki, T., Yoshida, S., Hatayama, M., Yamashita, S., Tanaka, Y., Motohashi, R., Denessiouk, K., Takahashi, S., Nakayama, T., 2018. Physical interactions among flavonoid enzymes in snapdragon and torenia reveal the diversity in the flavonoid metabolon organization of different plant species. Plant J. 94, 372-392.
  • Garg, R., Jain, M., 2013. RNA-Seq for transcriptome analysis in non-model plant. Methods Mol. Biol. 1069, 43-58.
  • Ghate, V., 1999. Bruhatpanchmula in ethno-medico and ayurved. J-AIM. 21, 1099-1110.
  • Gou, J.Y., Felippes, F.F., Liu, C.J., Weigel, D., Wang, J.W., 2011. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23, 1512-1522.
  • Gupta, R., Sharma, V., Sharma, N., Kumar, N., Singh, B., 2008. In vitro a ntioxidant activity from leaves of O roxylum indicum (L.) vent. A North indian highly threatened and vulnerable medicinal plant. J. Pharm. Res. 1, 65-72.
  • Harminder, Singh, V., Chaudhary, A.K., 2011. A review on the taxonomy, ethnobotany, chemistry and pharmacology of Oroxylum indicum vent. Indian J. Pharmaceut. Sci. 73, 483-490.
  • Hass, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., MacManes, M.D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C.N., Henschel, R., LeDuc, R.D., Friedman, N., Regev, A., 2013. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494-1512.
  • Hichri, I., Barrieu, F., Bogs, J., Kappel, C., Delrot, S., Lauvergeat, V., 2011. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J. Exp. Bot. 62, 2465-2483.
  • Jayaram, K., Prasad, M.N.V., 2008. Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a vulnerable medicinal plant by random amplified polymorphic DNA marker. Afr. J. Biotechnol. 7, 254-262.
  • Jimenez-Ruiz, J., Leyva-Perez, M., Schiliro, E., Barroso, J.B., Bombarely, A., Mueller, L., Mercado-Blanco, J., Luque, F., 2017. Transcriptomic analysis of Oleaeuropaea L. roots during the Verticillium dahliae early infection process. Plant Genome 10, 1-15.
  • Koirala, N., Thuan, N.H., Ghimire, G.P., Thang, D.V., Sohng, J.K., 2016. Methylation of flavonoids: chemical structures, bioactivities, progress and perspectives for biotechnological production. Enzym. Microb. Technol. 86, 103-116.
  • Krishnan, N.M., Pattnaik, S., Jain, P., Gaur, P., Choudhary, R., Vaidyanathan, S., Deepak, S., Hariharan, A.K., Krishna, P.G.B., Nair, J., Varghese, L., Valivarthi, N.K., Dhas, K., Ramaswamy, K., Panda, B., 2012. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachtaindica. BMC Genomics 13, 464-475.
  • Kumar, S., Pandey, A.K., 2013. Chemistry and biological activities of flavonoids: an Overview. Sci. World J. 2013, 162750. https://doi.org/10.1155/2013/162750.
  • Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870-1874. https://doi. org/10.1093/molbev/msw054.
  • Lang, T., Yin, K., Liu, J., Cao, K., Cannon, C.H., Du, F.K., 2014. Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus. PloS One 9 (9), e108719. https://doi.org/10.1371/journal.pone. 0108719.
  • Li, H., Fu, Y., Sun, H., Zhang, Y., Lan, X., 2017. Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum. Sci. Rep. 7, 74-84.
  • Li, S., 2014. Transcriptional control of flavonoid biosynthesis. Fine-tuning of the MYBbHLH-WD40 (MBW) complex. Plant Signal. Behav. 9, e27522.
  • Liu, Z., Tavares, R., Forsythe, E.S., Andre, F., Lugan, R., Jonasson, G., Mercey, S.B., Tohge, T., Beilstein, M.A., Daniele Werck-Reichhart, D.W., Renault, H., 2016. Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nat. Commun. 7, 13026. https://doi.org/10.1038/ncomms13026.
  • Liu, J., Hou, J., Jiang, C., Li, G., Lu, H., Meng, F., et al., 2015. Deep sequencing of the Scutellaria baicalensis Georgi transcriptome reveals flavonoid biosynthetic profiling and organ-specific gene expression. PloS One 10 (8), e0136397. https://doi.org/10. 1371/journal.pone.0136397.
  • Mano, H., Ogasawara, F., Sato, K., Higo, H., Minobe, Y., 2007. Isolation of a regulatory gene of anthocyanin biosynthesis in tuberous roots of purple-fleshed sweet potato. Plant Physiol. 143, 1252-1268.
  • Mazumdar, A.B., Chattopadhyay, S., 2016. Sequencing, de novo assembly, functional annotation and analysi of Phyllanthus amarus leaf transcriptome using the Illumina platform. Front. Plant Sci. 6, 1199. https://doi.org/10.3389/fpls.2015.01199.
  • Mehrtens, F., Kranz, H., Bednarek, P., Weisshaar, B., 2005. The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol. 138, 1083-1096.
  • Middleton, E., Kandaswami, C., Theoharides, T.C., 2000. The effects of plant flavonoids on mammalian cells: implications for inflammation, heart disease, and cancer. Pharmacol. Rev. 52, 673-751.
  • Narayana, K.R., Reddy, M.S., Chaluvadi, M.R., Krishna, D.R., 2001. Bioflavonoids classification, pharmacological, biochemical effects and therapeutic potential. Indian J. Pharmacol. 33, 2-16.
  • Nesi, N., Debeaujon, I., Jond, C., Stewart, A.J., Jenkins, G.I., Caboche, M., Lepiniec, L., 2002. The TRANSPARENT TESTA16 locus encodes the Arabidopsis bsistermads domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14, 2463-2479.
  • Noguchi, A., Saito, A., Homma, Y., Nakao, M., Sasaki, N., Nishino, T., Takahashi, S., Nakayama, T., 2007. A UDP-glucose: isoflavone 7-O-glucosyltransferase from the roots of soybean (Glycine max) seedlings. Purification, gene cloning, phylogenetics and an implication for an alternative strategy of enzyme catalysis. J. Biol. Chem. 282, 13581-23590.
  • Ozsolak, F., Milos, M., 2011. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98.
  • Park, Y., Li, X., Noh, S., Kim, J., Lim, S., Park, N., Kim, S., Kim, Y., Kim, Y., Lee, S., Arasu, M.V., Al-Dhabi, N.A., Park, S., 2016. Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei. BMC Genomics 17, 303-319.
  • Peer, W.A., Murphy, A.S., 2007. Flavonoids and auxin transport: modulators or regulators? Trends Plant Sci. 12, 556-563.
  • Reddy, N., Mehta, R.H., Soni, P.H., Makasana, J., Gajbhiye, N.A., Ponnuchamy, M., Kumar, J., 2015. Next generation sequencing and transcriptome analysis predicts biosynthetic pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a non-model plant with potent laxative properties. PloS One 10 (6), e0129422. https://doi. org/10.1371/journal.pone.0129422.
  • Reeksting, B.J., Coetzer, N., Mahomed, W., Engelbrecht, J., Berg, N., 2014. De Novo sequencing, assembly and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PloS One 9 (2), e86399. https:// doi.org/10.1371/journal.pone.0086399.
  • Roy, M.K., Nakahara, K., Thalang, V., Trakoontivakorn, G., Takenaka, M., Isobe, S., Tsushida, T., 2007. Baicalein, a flavonoid extracted from a methanolic extract of Oroxylumindicum inhibits proliferation of a cancer cell line in vitro via induction of apoptosis. Pharmazie 62, 149-153
  • Samantha, T., Shyamsundarachary, R., Srinivas, P., Swamy, N.R., 2012. Phytochemical analysis of seeds, stem, bark and root of an endangered medicinal forest tree Oroxylumindicum (L) Kurz. Int. J. Pharm. Biol. Sci. 3, 1063-1075.
  • Shankar, D., Ved, D.K., 2003. A balanced perspective of management of Indian medicinal plants. Indian For. 129, 275-288.
  • Shi, C.Y., Yang, H., Wei, C.L., Yu, O., Zhang, Z.Z., Jiang, C.J., Sun, J., Li, Y.Y., Chen, Q., Xia, T., Wan, X.C., 2011. Deep sequencing of the Camelliasinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12, 131-150.
  • Srithongchuay, T., Bumrungsri, S., Sripao-raya, E., 2008. The pollination ecology of the late-successional tree, Oroxylum indicum(Bignoniaceae) in Thailand. J. Trop. Ecol. 24, 477-484.
  • Stracke, R., Ishihara, H., Huep, G., Barsch, A., Mehrtens, F., Niehaus, K., Weisshaar, B., 2007. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J. 50, 660-677.
  • Strickler, S.R., Bombarely, A., Mueller, L.A., 2012. Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am. J. Bot. 1999, 257-266.
  • Taylor, L.P., Grotewold, E., 2005. Flavonoids as developmental regulators. Curr. Opin. Plant Biol. 8, 317-323.
  • Terrier, N., Torregrosa, L., Ageorges, A., Vialet, S., Verries, C., Cheynier, V., Romieu, C., 2009. Ectopic expression of VvMybPA2 promotes proanthocyanid in biosynthesis in grapevine and suggests additional targets in the pathway. Plant Physiol. 149, 1028-1041.
  • Tiwari, S., Shah, K., Shah, P., 2007. In vitro propagation of Oroxylum indicum- an endangered medicinal tree. Biotechnology 6, 299-301.
  • Torre, S., Tattini, M., Brunetti, C., Guidi, L., Gori, A., Marzano, C., Landi, M., Sebastiani, F., 2016. De Novo assembly and comparative transcriptome analyses of red and green morphs of sweet basil grown in full sunlight. PloS One 11 (8), e0160370. https://doi. org/10.1371/journal.pone.0160370.
  • Verslues, P.E., Lasky, J.R., Juenger, T.E., Liu, T.W., Kumar, M.N., 2014. Genome wide association mapping combined with reverse genetics identifies new effectors of low water potential induced proline accumulation in Arabidopsis. Plant Physiol. 164, 144-159.
  • Vom Endt, D., Kijne, J.W., Memelink, J., 2002. Transcription factors controlling plant secondary metabolism: what regulates the regulators? Phytochemistry 6, 107-114.
  • Wang, X., 2011. Structure, function, and engineering of enzymes in isoflavonoid biosynthesis. Funct. Integr. Genom. 1, 13-22. https://doi.org/10.1007/s10142-010- 0197-9. Epub 2010 Oct 30.
  • Wang, Z., Gerstein, M., Snyder, M., 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
  • Wu, J., Wang, X.C., Liu, Y., Du, H., Shu, Q.Y., Su, S., Wang, L.J., Li, S.S., Wang, L.S., 2016. Flavone synthases from Lonicera japonica and L. macranthoides reveal differential flavones accumulation. Sci. Rep. 6, 1-14.
  • Yasodha, R., Ghosh, M., Santan, B., Gurumurthi, K., 2004. Importance of biotechnological research in tree species of Dashmula. Indian For. 130, 79-88.
  • Zaveri, M., Gohil, P., Jain, S., 2006. Immunostimulant activity of n -butanol fraction of root bark of Oroxylum indicum, vent. J. Immunotoxicol. 3, 83-99.
  • Zhang, Q., Zhao, X., Qiu, H., 2013. Flavones and flavonols: phytochemistryand biochemistry. In: Ramawat, K.G., Merillon, J.-M. (Eds.), Natural Products: Phytochemistry, Botany and Metabolism of Alkaloids, Phenolics and Terpenes. Springer, Berlin Heidelberg, pp. 1821-1847.
  • Zhao, Q., Cui, M.Y., Levsh, O., Yang, D.,J., Li, J., Hill, L., Yang, L., Hu, Y., Weng, J.-K., Chen, X.-Y., Martin, C., 2018. Two CYP82D enzymes function as flavone hydroxylases in the biosynthesis of root-Specific 4'-deoxyflavones in Scutellaria baicalensis. Mol. Plant 11, 135-148.
  • Zhao, Q., Zhang, Y., Wang, G., Hill, L., Weng, J.K., Chen, X.Y., Xue, H., Martin, C., 2016. A specialized flavone biosynthetic pathway has evolved in the medicinal plant, Scutellaria baicalensis. Sci. Adv. 2, e1501780. https://doi.org/10.1126/sciadv. 1501780.
  • Zuk, M., Dzialo, M., Richter, D., Dyminska, L., Matula, J., Kotecki, A., Hanuza, J., Szopa, J., 2016. Chalcone synthase (CHS) gene suppression in flax leads to changes in wall synthesis and sensing genes, cell wall chemistry and stem morphology parameters. Front. Plant Sci. 7, 894. https://doi.org/10.3389/fpls.2016.00894.