High-throughput sequencing and de novo assembly of the Isatis indigotica transcriptome

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Tang, Xiaoqing ^a   Xiao, Yunhua ^a   Lv, Tingting ^a   Wang, Fangquan ^b   Zhu, Qian Hao ^c   Zheng, Tianqing ^d   Yang, Jie ^b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c CSIRO   (Australia)

^d INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICROSATELLITE DNA; TRANSCRIPTOME;

ARTICLE; HIGH THROUGHPUT SEQUENCING; ISATIS INDIGOTICA; MEDICINAL PLANT; NONHUMAN; PLANT GENE; PLANT LEAF; PLANT ROOT; RNA SEQUENCE; SIMPLE SEQUENCE REPEAT; TRANSCRIPTOMICS; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; ISATIS; METABOLISM; MOLECULAR GENETICS; SIGNAL TRANSDUCTION;

ISATIS TINCTORIA;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; ISATIS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; PLANTS, MEDICINAL; SIGNAL TRANSDUCTION; TRANSCRIPTOME;

EID: 84907914057     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0102963     Document Type: Article

References (37)

1. National Pharmacopoeia Committee (2010) Pharmacopoeia of the People's Republic of China. China Medical Science and Technology Press. Beijing 20, 191.
2. Lin CW, Tsai FJ, Tsai CH, Lai CC, Wan L, et al. (2005) Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds. Antiviral Research 68: 36-42.
3. Hsuan SL, Chang SC, Wang SY, Liao TL, Jong TT, et al. (2009) The cytotoxicity to leukemia cells and antiviral effects of Isatis indigotica extracts on pseudorabies virus. J Ethnopharmacology 123: 61-67.
4. Sun DD, Dong WW, Li X, Zhang HQ (2010) Indole alkaloids from the roots of Isatis indigotica and their antiherpes simlex virus type 2(HSV-2) activity in vitro. Chem Natural Comounds 46: 763-766.
5. Xia XZ, Xiao J, Shi GF, Li WH (2007) Research of resistance to Salmonella typhimurium infection using Banlangen polysaccharide. Medical J Wuhan University 28: 348-350.
6. Liu YH, Wu XY, Fang JG, Tang J (2003) Studies on chemical constituents from Radix Isatidis. Herbal of Medicine 22: 591-594.
7. Liu JJ, Huang RW, Lin DJ, Wu XY, Lin Q (2005) Antiproliferation effects of ponicidin on human myeloid leukemia cells in vitro. Oncology Reports 13: 653-657.
8. Kunikata T, Tatefuji T, Aga H, Iwak K, Ikeda M, Kurimoto M (2000) Indirubin inhibits inflammatory reactions in delayed-type hypersensitivity. European J - Pharmacology 410: 93-100.
9. Ho YL, Chang YS (2002) Studies on the antinociceptive, anti-inflammatory and antipyretic effects of Isatis indigotica root. Phytomedicine 9: 419-424.
10. Chen L, Lin T, Zhang HX, Su YB (2005) Immune response to foot-and-mouth disease DNA vaccines can be enhanced by coinjection with the Isatis indigotica extract. Intervirology 48: 207-212.
11. Wu XY, Qin GW, Cheung KK, Cheng KF (1997) New alkaloids from Isatis indigotica. Tetrahedron 53: 13323-13328.
12. Wu XY, Liu YH, Sheng WY, Sun J, Qin GW (1997). Chemical constituents of Isatis indigotica. Planta Med 63: 55-57.
13. Wu YX, Zhang ZX, Hu H, Li DM, Qiu GF, et al. (2011) Novel indole C-glycosides from Isatis indigotica and their potential cytotoxic activity. Fitoterapia 82: 288-292.
14. Xu H, Fang JG, Wang SB, Liu YW (2003) Studies on the chemical constituents of Isatis indigotica in root. Chin Pharm J 38: 418-419.
15. Liu YH, Fang JG, Gong XP, Xie W (2003) Anti-endotoxic effects of syringic acid in Radix Isatidis. Chinese Traditional and Herbal Drugs 34: 926-928.
16. Liu YH, Qin GW, Ding SP, Wu XY (2002) Studies on chemical constituents in root of Isatis indigotica III, Chinese Traditional and Herbal Drugs 33: 97-99.
17. Liu HL, Wu LJ, Wu B (2002) Studies on the plane structure of indigoticoside A. Chinese J Magnetic Resonance 19: 315-319.
18. Stoker KG (1997) The cultivation of woad (Isatis tinctoria) for production of natural indigo: agronomy, extraction and biochemical aspects. PhD thesis, University of Bristol, UK.
19. Giorgia Spataro, Paola Taviani and Valeria Negri (2007) Genetic variation and population structure in a Eurasian collection of Isatis tinctoria L. Genetic Resources and Crop Evolution 54: 573-584.
20. Salvini M, Boccardi TM, Sani E, Bernardi R, Tozzi S, et al.(2008) Alpha-tryptophan synthase of Isatis tinctoria: gene cloning and expression. Plant Physiology and Biochemistry 46: 715-723.
21. Fortune R (1846) The notice of the tein-ching or chinese indigo. J Roy Hort Soc 1: 269-271.
22. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6(5): 377-382.
23. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45-58.
24. Zhu QH, Stephen S, Taylor J, Helliwell CA, Wang MB (2014) Long non-coding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol 201: 574-584.
25. Wilhelm BT, Marguerat S, Goodhead I, Bahler J (2010) Defining transcribed regions using RNA-seq. Nat Protoc 5(2): 255-266.
26. Feng C, Chen M, Xu C, Bai L, Yin X, et al. (2012) Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RANSeq. BMC Genomics. 13: 19.
27. Zhang XM, Zhao L, Larson-Rabin Z, Guo ZH (2012) De Novo Sequenceing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus(Poaceae: Bambusoideae). PloS ONE 7: e42082.
28. Xia ZH, Xu HM, Zhai JL, Li DJ, Luo HL, et al. (2011) RNA-seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77: 299-308.
29. Zou D, Chen XB, Zou DS (2013) Sequencing de novo assembly, annotation and SSR and SNP detection of sabaigrass (Eulaliopsis binata) transcriptome. Genomics 102: 57-62.
30. Platel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7(2): e30619.
31. Manfred G Grabhere, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, et al. (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29: 644-652.
32. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, et al. (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
33. Lu ShSh, Jia RR, Duan F, Liu ZP, Yu JN (2011) Cloning and expression analysis under stress of IiLEA Gene in Isatis indigotica. Acta Bot Boreal - Occident Sin 31: 0511-0516.
34. Sun XD, Li AL, Han LM (2012) Cloning and identification of APX gene from Isatis indigotica. Guihaia 32: 367-370.
35. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceeding/international conference on intelligent systems for molecular biology, ISMB, 138-148.
36. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2 GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18): 3674-3676.
37. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue): W293-W297.