Transcriptomic landscape of pueraria lobata demonstrates potential for phytochemical study

Frontiers in Plant Science

Volumn 6, Issue JUNE, 2015, Pages 1-10

  Han, Rongchun ^a,b   Takahashi, Hiroki ^a   Nakamura, Michimi ^a   Yoshimoto, Naoko ^a   Suzuki, Hideyuki ^c   Shibata, Daisuke ^c   Yamazaki, Mami ^a   Saito, Kazuki ^a  

^a CHIBA UNIVERSITY   (Japan)

^b LIAONING UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

^c KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

Deep transcriptome analysis; Kudzu; Leguminosae; Pueraria lobata

Indexed keywords

FABACEAE; PUERARIA MONTANA VAR. LOBATA;

EID: 84934965088     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00426     Document Type: Article

References (44)

1. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29. doi: 10.1038/75556
2. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate – a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol. 57, 289–300
3. Bouque, V., Bourgaud, F., Nguyen, C., and Guckert, A. (1998). Production of daidzein by callus cultures of Psoralea species and comparison with plants. Plant Cell Tissue Organ Cult. 53, 35–40. doi: 10.1023/A:1006057211490
4. Brazier-Hicks, M., Evans, K. M., Gershater, M. C., Puschmann, H., Steel, P. G., and Edwards, R. (2009). The C-glycosylation of flavonoids in cereals. J. Biol. Chem. 284, 17926–17934. doi: 10.1074/jbc.M109.009258
5. Carai, M. A., Agabio, R., Bombardelli, E., Bourov, I., Gessa, G. L., Lobina, C., et al. (2000). Potential use of medicinal plants in the treatment of alcoholism. Fitoterapia 71, S38–S42. doi: 10.1016/S0367-326X(00)00178-7
6. Chen, G., Zhang, J., and Jiannong, Y. (2001). Determination of puerarin, daidzein and rutin in Pueraria lobata (Wild.) Ohwi by capillary electrophoresis with electrochemical detection. J. Chromatogr. A 923, 255–262. doi: 10.1016/S0021-9673(01)00996-7
7. Chen, H., and Boutros, P. C. (2011). VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform. 12:35. doi: 10.1186/1471-2105-12-35
8. Cherdshewasart, W., Subtang, S., and Dahlan, W. (2007). Major isoflavonoid contents of the phytoestrogen rich-herb Pueraria mirifica in comparison with Pueraria lobata. J. Pharm. Biomed. Anal. 43, 428–434. doi: 10.1016/j.jpba.2006.07.013
9. Cherdshewasart, W., and Sutjit, W. (2008). Correlation of antioxidant activity and major isoflavonoid contents of the phytoestrogen-rich Pueraria mirifica and Pueraria lobata tubers. Phytomedicine 15, 38–43. doi: 10.1016/j.phymed.2007.07.058
10. Falcone Ferreyra, M. L., Rius, S. P., and Casati, P. (2012). Flavonoids: biosynthesis, biological functions, and biotechnological applications. Front. Plant Sci. 3:222. doi: 10.3389/fpls.2012.00222
11. Ferreyra, M. L. F., Rodriguez, E., Casas, M. I., Labadie, G., Grotewold, E., and Casati, P. (2013). Identification of a bifunctional maize C-and O-Glucosyltransferase. J. Biol. Chem. 288, 31678–31688. doi: 10.1074/jbc.M113.510040
12. Follak, S. (2011). Potential distribution and environmental threat of Pueraria lobata. Cent. Eur. J. Biol. 6, 457–469. doi: 10.2478/s11535-010-0120-3
13. Fu, L., Niu, B., Zhu, Z., Wu, S., and Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152. doi: 10.1093/bioinformatics/bts565
14. Fullwood, M. J., Wei, C. L., Liu, E. T., and Ruan, Y. (2009). Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19, 521–532. doi: 10.1101/gr.0749 06.107
15. Gaines, T. A., Lorentz, L., Figge, A., Herrmann, J., Maiwald, F., Ott, M. C., et al. (2014). RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum. Plant J. 78, 865–876. doi: 10.1111/tpj.12514
16. Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652. doi: 10.1038/nbt.1883
17. Graham, T. L. (1991). Flavonoid and isoflavonoid distribution in developing soybean seedling tissues and in seed and root exudates. Plant Physiol. 95, 594–603. doi: 10.1104/Pp.95.2.594
18. Han, R., Takahashi, H., Nakamura, M., Bunsupa, S., Yoshimoto, N., Yamamoto, H., et al. (2015). Transcriptome analysis of nine tissues to discover genes involved in the biosynthesis of active ingredients in Sophora flavescens. Biol. Pharm. Bull. 38, 876–883. doi: 10.1248/bpb.b14-00834
19. He, X., Blount, J. W., Ge, S., Tang, Y., and Dixon, R. A. (2011). A genomic approach to isoflavone biosynthesis in kudzu (Pueraria lobata). Planta 233, 843–855. doi: 10.1007/s00425-010-1344-1
20. He, X. Z., Li, W. S., Blount, J. W., and Dixon, R. A. (2008). Regioselective synthesis of plant (iso)flavone glycosides in Escherichia coli. Appl. Microbiol. Biotechnol. 80, 253–260. doi: 10.1007/s00253-008-1554-7
21. Hong, S. M., Bahn, S. C., Lyu, A., Jung, H. S., and Ahn, J. H. (2010). Identification and testing of superior reference genes for a starting pool of transcript normalization in Arabidopsis. Plant Cell Physiol. 51, 1694–1706. doi: 10.1093/pcp/pcq128
22. Jung, W., Yu, O., Lau, S. M., O’keefe, D. P., Odell, J., Fader, G., et al. (2000). Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nat. Biotechnol. 18, 208–212. doi: 10.1038/72671
23. Kawaguchi, R., and Bailey-Serres, J. (2005). mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res. 33, 955–965. doi: 10.1093/Nar/Gki240
24. Kerscher, F., and Franz, G. (1987). Biosynthesis of vitexin and isovitexin – enzymatic synthesis of the C-glucosylflavones vitexin and isovitexin with an enzyme preparation from Fagopyrum esculentum m. seedlings. Z. Naturforsch. 42, 519–524.
25. Keung, W. M., and Vallee, B. L. (1998). Kudzu root: an ancient Chinese source of modern antidipsotropic agents. Phytochemistry 47, 499–506. doi: 10.1016/S0031-9422(97)00723-1
26. Li, R., Yu, C., Li, Y., Lam, T. W., Yiu, S. M., Kristiansen, K., et al. (2009). SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967. doi: 10.1093/bioinformatics/btp336
27. Lindgren, C. J., Castro, K. L., Coiner, H. A., Nurse, R. E., and Darbyshire, S. J. (2013). The biology of invasive alien plants in Canada. 12. Pueraria montana var. lobata (Willd.) Sanjappa & Predeep. Can. J. Plant Sci. 93, 71–95. doi: 10.4141/Cjps2012-128
28. Miadokova, E. (2009). Isoflavonoids – an overview of their biological activities and potential health benefits. Interdiscip. Toxicol. 2, 211–218. doi: 10.2478/v10102-009-0021-3
29. Miyazawa, M., Sakano, K., Nakamura, S., and Kosaka, H. (2001). Antimutagenic activity of isoflavone from Pueraria lobata. J. Agric. Food Chem. 49, 336–341. doi: 10.1021/jf000255w
30. Muranaka, T., and Saito, K. (2013). Phytochemical genomics on the way. Plant Cell Physiol. 54, 645–646. doi: 10.1093/Pcp/Pct058
31. Ramilowski, J. A., Sawai, S., Seki, H., Mochida, K., Yoshida, T., Sakurai, T., et al. (2013). Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals. Plant Cell Physiol. 54, 697–710. doi: 10.1093/pcp/pct057
32. Saito, K. (2013). Phytochemical genomics – a new trend. Curr. Opin. Plant Biol. 16, 373–380. doi: 10.1016/j.pbi.2013.04.001
33. Saito, K., Yonekura-Sakakibara, K., Nakabayashi, R., Higashi, Y., Yamazaki, M., Tohge, T., et al. (2013). The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiol. Biochem. 72, 21–34. doi: 10.1016/j.plaphy.2013.02.001
34. Schmittgen, T. D., and Livak, K. J. (2008). Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108. doi: 10.1038/nprot.2008.73
35. Serres-Giardi, L., Belkhir, K., David, J., and Glemin, S. (2012). Patterns and evolution of nucleotide landscapes in seed plants. Plant Cell 24, 1379–1397. doi: 10.1105/tpc.111.093674
36. Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J., and Birol, I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123. doi: 10.1101/gr.089532.108
37. Steele, C. L., Gijzen, M., Qutob, D., and Dixon, R. A. (1999). Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean. Arch. Biochem. Biophys. 367, 146–150. doi: 10.1006/abbi.1999.1238
38. Takahashi, H., Morioka, R., Ito, R., Oshima, T., Altaf-Ul-Amin, M., Ogasawara, N., et al. (2011). Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach. OMICS 15, 15–23. doi: 10.1089/omi.2010.0074
39. Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A., and Conesa, A. (2011). Differential expression in RNA-seq: a matter of depth. Genome Res. 21, 2213–2223. doi: 10.1101/gr.124321.111
40. Teng, Y., Cui, H., Yang, M., Song, H., Zhang, Q., Su, Y., et al. (2009). Protective effect of puerarin on diabetic retinopathy in rats. Mol. Biol. Rep. 36, 1129–1133. doi: 10.1007/s11033-008-9288-2
41. Tian, A. G., Wang, J., Cui, P., Han, Y. J., Xu, H., Cong, L. J., et al. (2004). Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor. Appl. Genet. 108, 903–913. doi: 10.1007/s00122-003-1499-2
42. Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63. doi: 10.1038/nrg2484
43. Wong, K. H., Li, G. Q., Li, K. M., Razmovski-Naumovski, V., and Chan, K. (2011). Kudzu root: traditional uses and potential medicinal benefits in diabetes and cardiovascular diseases. J. Ethnopharmacol. 134, 584–607. doi: 10.1016/j.jep.2011.02.001
44. Ye, J., Fang, L., Zheng, H. K., Zhang, Y., Chen, J., Zhang, Z. J., et al. (2006). WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34, W293–W297. doi: 10.1093/Nar/Gkl1031