Abstract
Indigo is the most important blue dye for textile dyeing and is biosynthesized in Polygonum tinctorium. Some biochemical studies related to biosynthesis are available. However, genomic and transcriptome studies have not received sufficient attention. Here, we report de novo assembly of transcriptome datasets and its comprehensive analysis. A total of 60,395 unigenes were annotated using BLAST search against the different databases. At least 23,721 unigenes mapped onto different pathways using KEGG database. We found that 3,323 genes are involved in biosynthesis of secondary metabolites, 117 phenylalanine, tyrosine and tryptophan biosynthesis and 147 tryptophan metabolisms. Apart from this, indigo biosynthesis pathway genes viz., dioxygenase, monooxygenase, and glucosyltransferase have also been identified. Fourteen genes encoding cytochrome P450 monooxygenase, 26 glucoside dioxygenase, 9 UDP-glucose D-glucosyltransferase and 52 were β-D-glucosidase. These findings provide a foundation for further analysis of this pathway with potential to enhance the synthesis of indican in P. tinctorium
References
Conesa A., Gotz S., Garrcia-Gomez M., Terol J., Talon M. & Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.10.1093/bioinformatics/bti610Suche in Google Scholar
Bioinformatics 21: 3674-3676.Suche in Google Scholar
Ensley B.D., Ratzkin B.J., Osslund T.D., Simon M.J., Wackett L.P. & Gibson D.T. 1983. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 222: 167-169.10.1126/science.6353574Suche in Google Scholar
Epstein E., Nabors M.W. & Stowe B.B. 1967. Origin of indigo of woad. Nature 216: 547-549.10.1038/216547a0Suche in Google Scholar
Garg R., Patel R.K., Tyagi A.K. & Jain M. 2011. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18: 53-63.10.1093/dnares/dsq028Suche in Google Scholar
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N. & Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol. 29: 644-652.10.1038/nbt.1883Suche in Google Scholar
Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T. & Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36: D480-D484.10.1093/nar/gkm882Suche in Google Scholar
Kim J.Y., Lee J.Y., Shin Y. & Kim G.J. 2010. Characterization of an indicant-hydrolyzing enzyme from Sinorhizobium meliloti. Process Biochem. 45: 892-896.10.1016/j.procbio.2010.02.017Suche in Google Scholar
Kudapa H., Bharti A.K., Cannon S.B., Farmer A.D., Mulaosmanovic B., Kramer R., Bohra A., Weeks N.T., Crow J.A., Tuteja R., Shah T., Dutta S., Gupta D.K., Singh A., Gaikwad K., Sharma T.R., May G.D., Singh N.K. & Varshney R.K. 2012. A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms. Mol. Plant. 5: 1020-1028.10.1093/mp/ssr111Suche in Google Scholar
Lee C.Y. & Kim W.J. 1990. Production of natural colorants by plant cell biotechnology, pp. 81-85. In: Natural Spices and Pigments (in Korean), Hyangmoon Publishing Co., Seoul, Korea.Suche in Google Scholar
Marcinek H., Weyler W., Deus-Neumann B. & Zenk M.H. 2000. Indoxyl-UDPG-glucosyltransferase from Baphicacanthus cusia. Phytochemistry 53: 201-207.10.1016/S0031-9422(99)00430-6Suche in Google Scholar
Maugard T., Enaud E., Sayette A.L., Choisy P. & Legoy M.D. 2002. β-Glucosidase catalysed hydrolysis of indican from leaves of Polygonum tinctorium. Biotechnol. Progr. 18: 1104-1108.10.1021/bp025540+Suche in Google Scholar PubMed
Minami Y., Kanafuji T. & Miura K. 1996. Purification and characterization of a β-glucosidase from Polygonum tinctorium, which catalyzes preferentially the hydrolysis of indican. Biosci. Biotech. Biochem. 60: 147-149.Suche in Google Scholar
Minami Y., Nishimura O., Hara-Nishimura I., Nishimura M. & Matsubara H. 2000. Tissue and intracellular localization of indican and the purification and characterization of indican synthase from indigo plants. Plant Cell Physiol. 41: 218-225.10.1093/pcp/41.2.218Suche in Google Scholar PubMed
Minami Y., Shigeta Y., Tokumoto U., Tanaka Y., Yonekura- Sakakibara K. & Ohoka H. 1999. Cloning, sequencing, characterization, and expression of a β-glucosidase cDNA from the indigo plant. Plant Sci. 142: 219-226.Suche in Google Scholar
Minami Y., Takao H., Kanafuji T., Miura K., Kondo M., Hara- Nishimura I., Nishimura M. & Matsubara, H. 1997. β- Glucosidase in the indigo plant: intracellular localization and tissue specific expression in leaves. Plant Cell Physiol. 38: 1069-1074.10.1093/oxfordjournals.pcp.a029273Suche in Google Scholar PubMed
Peng H. & Zhang J. 2009. Commercial high-throughput sequencing and its applications in DNA analysis. Biologia 64: 20-26.10.2478/s11756-009-0028-4Suche in Google Scholar
Schullehner K., Dick R., Vitzthum F., Schwab W., Brandt W., Frey M. & Gierl A. 2008. Benzoxazinoid biosynthesis in dicot plants. Phytochemistry 69: 2668-2677.10.1016/j.phytochem.2008.08.023Suche in Google Scholar PubMed
Shin Y., Yoo D.I. & Kim K. 2012. Process balance of natural indigo production based on traditional Niram method. Textile Coloration and Finishing 24: 253-259.10.5764/TCF.2012.24.4.253Suche in Google Scholar
Song K.S., Shim J.Y., Jung D.S. & Kim S.U. 2011. Origin of oxygen in indoxyl-derivatives of Polygonum tinctorium L. as probed by 18O2 feeding. J. Korean Soc. Appl. Biol. Chem. 54: 340-344.10.3839/jksabc.2011.054Suche in Google Scholar
Stoker K.G., Cooke D.T. & Hill D.J. 1998. An improved method for the large-scale processing of woad (Isatis tinctoria) for possible commercial production of woad indigo. J. Agric. Eng. Res. 7: 315-320.10.1006/jaer.1998.0329Suche in Google Scholar
Tatusov R.L., Galperin M.Y., Natale D.A. & Koonin E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36.10.1093/nar/28.1.33Suche in Google Scholar PubMed PubMed Central
Thudi M., Li Y., Jackson S.A., May G.D. & Varshney R.K. 2012. Current state-of-art of sequencing technologies for plant genomic research. Brief. Funct. Genomics 11: 3-11.10.1093/bfgp/elr045Suche in Google Scholar PubMed
Troncoso-Ponce M.A., Kilaru A., Cao X., Durrett T.P., Fan J., Jensen J.K., Thrower N.A., Pauly M., Wilkerson C. & Ohlrogge J.B. 2011. Comparative deep transcriptional profiling of four developing oilseeds. Plant J. 68: 1014-1027.10.1111/j.1365-313X.2011.04751.xSuche in Google Scholar PubMed PubMed Central
Ye J., Fang L., Zheng H.K., 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. 10.1093/nar/gkl031Suche in Google Scholar PubMed PubMed Central
© 2016
Artikel in diesem Heft
- Down into the Earth: microbial diversity of the deepest cave of the world
- Factors influencing synergistic antimicrobial activity of thymol and nisin against Shigella spp. in sugarcane juice
- Effects of low-temperature hardening on the biochemical response of winter oilseed rape seedlings inoculated with the spores of Leptosphaeria maculans
- Mitochondrial structures during seed germination and early seedling development in Arabidopsis thaliana
- Transcriptome analysis for identification of indigo biosynthesis pathway genes in Polygonum tinctorium
- Different components of plant diversity suggest the protection of a large area for the conservation of a riparian ecosystem
- Anatomical adaptations of the desert species Stipa lagascae against drought stress
- Effects of ammonium ion on cell growth and biosynthesis of shikonin derivatives in callus tissues of Arnebia euchroma
- cDNA cloning, heterologous expression and characterization of a cell wall invertase from copper tolerant population of Elsholtzia haichowensis
- Construction of cDNA library from Prunus campanulata leaves and preliminary expressed sequence tag (EST) analysis during cold stress
- Phylogenetic utility of the geometric model of the body form in leeches (Clitellata: Hirudinida)
- Substrate choice by the alien snail Ferrissia fragilis (Gastropoda: Planorbidae) in an industrial area: A case study in a forest pond (Southern Poland)
- History of two critically endangered grassland snails (Pulmonata: Helicellinae) in the Czech Republic with first molecular data on extinct populations
- Monteustium marezensis gen. n., sp. n. and the first record of Italustiun eframi (Acari: Prostigmata: Erythraeidae: Balaustiinae) from Montenegro
- Lithobius (Ezembius) laevidentata sp. n., a new species (Chilopoda: Lithobiomorpha: Lithobiidae) from the Northwest region of China
- Aphids in jeopardy? Aphid communities on xerothermic habitats
- Habitat and weather requirements of diurnal raptors wintering in river valleys
Artikel in diesem Heft
- Down into the Earth: microbial diversity of the deepest cave of the world
- Factors influencing synergistic antimicrobial activity of thymol and nisin against Shigella spp. in sugarcane juice
- Effects of low-temperature hardening on the biochemical response of winter oilseed rape seedlings inoculated with the spores of Leptosphaeria maculans
- Mitochondrial structures during seed germination and early seedling development in Arabidopsis thaliana
- Transcriptome analysis for identification of indigo biosynthesis pathway genes in Polygonum tinctorium
- Different components of plant diversity suggest the protection of a large area for the conservation of a riparian ecosystem
- Anatomical adaptations of the desert species Stipa lagascae against drought stress
- Effects of ammonium ion on cell growth and biosynthesis of shikonin derivatives in callus tissues of Arnebia euchroma
- cDNA cloning, heterologous expression and characterization of a cell wall invertase from copper tolerant population of Elsholtzia haichowensis
- Construction of cDNA library from Prunus campanulata leaves and preliminary expressed sequence tag (EST) analysis during cold stress
- Phylogenetic utility of the geometric model of the body form in leeches (Clitellata: Hirudinida)
- Substrate choice by the alien snail Ferrissia fragilis (Gastropoda: Planorbidae) in an industrial area: A case study in a forest pond (Southern Poland)
- History of two critically endangered grassland snails (Pulmonata: Helicellinae) in the Czech Republic with first molecular data on extinct populations
- Monteustium marezensis gen. n., sp. n. and the first record of Italustiun eframi (Acari: Prostigmata: Erythraeidae: Balaustiinae) from Montenegro
- Lithobius (Ezembius) laevidentata sp. n., a new species (Chilopoda: Lithobiomorpha: Lithobiidae) from the Northwest region of China
- Aphids in jeopardy? Aphid communities on xerothermic habitats
- Habitat and weather requirements of diurnal raptors wintering in river valleys