Global transcriptome analysis of al-induced genes in an al-accumulating species, common buckwheat (Fagopyrum esculentum Moench)

Plant and Cell Physiology

Volumn 55, Issue 12, 2014, Pages 2077-2091

  Yokosho, Kengo ^a   Yamaji, Naoki ^a   Ma, Jian Feng ^a  

^a OKAYAMA UNIVERSITY   (Japan)

Author keywords

Aluminum stress; Buckwheat; RNA Seq; Transcriptome; Transporter

Indexed keywords

ARABIDOPSIS; FAGOPYRUM ESCULENTUM;

ALUMINUM;

ARABIDOPSIS; DRUG EFFECTS; FAGOPYRUM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PLANT LEAF; PLANT ROOT; SEQUENCE ANALYSIS;

ALUMINUM; ARABIDOPSIS; BASE SEQUENCE; FAGOPYRUM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PLANT LEAVES; PLANT ROOTS; SEQUENCE ANALYSIS, RNA;

EID: 84922452050     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcu135     Document Type: Article

References (37)

1. Cardoso-Silva, C.B., Costa, E.A., Mancini, M.C., Balsalobre, T.W., Canesin, L.E., Pinto, L.R. et al. (2014) De novo assembly and transcriptome analysis of contrasting sugarcane varieties. PLoS One 9: e88462.
2. Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown, M.K. et al. (2008) Stem cell transcriptome profiling via massive- scale mRNA sequencing. Nat. Methods 5: 613-619.
3. Delhaize, E., Ma, J.F. and Ryan, P.R. (2012) Transcriptional regulation of aluminium tolerance genes. Trends Plant Sci. 17: 341-348.
4. Franceschi, V.R. and Nakata, P.A. (2005) Calcium oxalate in plants: formation and function. Annu. Rev. Plant Biol. 56: 41-71.
5. Huang, C.F., Yamaji, N., Chen, Z.C. and Ma, J.F. (2012) A tonoplast-localized half-size ABC transporter is required for internal detoxification of aluminum in rice. Plant J. 69: 857-867.
6. Huang, C.F., Yamaji, N. and Ma, J.F. (2010) Knockout of a bacterial-type ATP-binding cassette transporter gene, AtSTAR1, results in increased aluminum sensitivity in Arabidopsis. Plant Physiol. 153: 1669-1677.
7. Huang, C.F., Yamaji, N., Mitani, N., Yano, M., Nagamura, Y. and Ma, J.F. (2009) A bacterial-type ABC transporter is involved in aluminum tolerance in rice. Plant Cell 21: 655-667.
8. Iuchi, S., Koyama, H., Iuchi, A., Kobayashi, Y., Kitabayashi, S., Kobayashi, Y. et al. (2007) Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proc. Natl Acad. Sci. USA 104: 9900-9905.
9. Klug, B. and Horst, W.J. (2010a) Spatial characteristics of aluminium uptake and translocation in roots of buckwheat (Fagopyrum esculentum Moench). Physiol. Plant. 139: 181-191.
10. Klug, B. and Horst, W.J. (2010b) Oxalate exudation into the root-tip water free space confers protection from aluminum toxicity and allows aluminum accumulation in the symplast in buckwheat (Fagopyrum esculentum). New Phytol. 187: 380-391.
11. Larsen, P.B., Cancel, J., Rounds, M. and Ochoa, V. (2007) Arabidopsis ALS1 encodes a root tip and stele localized half type ABC transporter required for root growth in an aluminum toxic environment. Planta 225: 1447-1458.
12. Larsen, P.B., Geisler, M.J., Jones, C.A., Williams, K.M. and Cancel, J.D. (2005) ALS3 encodes a phloem-localized ABC transporter-like protein that is required for aluminum tolerance in Arabidopsis. Plant J. 41: 353-363.
13. Liu, J.P., Magalhaes, J.V., Shaff, J. and Kochian, L.V. (2009) Aluminumactivated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance. Plant J. 57: 389-399.
14. Logacheva, M.D., Kasianov, A.S., Vinogradov, D.V., Samigullin, T.H., Gelfand, M.S., Makeev, V.J. et al. (2011) De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 12: 30.
15. Ma, J.F. (2000) Role of organic acids in detoxification of aluminum in higher plants. Plant Cell Physiol. 41: 383-390.
16. Ma, J.F. and Hiradate, S. (2000) Form of aluminium for uptake and translocation in buckwheat (Fagopyrum esculentum Moench). Planta 211: 355-360.
17. Ma, J.F., Hiradate, S. and Matsumoto, H. (1998) High aluminum resistance in buckwheat-II. Oxalic acid detoxifies aluminum internally. Plant Physiol. 117: 753-759.
18. Ma, J.F., Ryan, P.R. and Delhaize, E. (2001) Aluminium tolerance in plants and the complexing role of organic acids. Trends Plant Sci. 6: 273-278.
19. Ma, J.F., Zheng, S.J., Matsumoto, H. and Hiradate, S. (1997) Detoxifying aluminium with buckwheat. Nature 390: 569-570.
20. Morozova, O., Hirst, M. and Marra, M.A. (2009) Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 10: 135-151.
21. Negishi, T., Oshima, K., Hattori, M., Kanai, M., Mano, S., Nishimura, M. et al. (2012) Tonoplast- and plasma membrane-localized aquaporin-family transporters in blue hydrangea sepals of aluminum hyperaccumulating plant. PLoS One 7: e43189.
22. Peng, Y., Gao, X., Li, R. and Cao, G. (2014) Transcriptome sequencing and de novo analysis of Youngia japonica using the Illumina platform. PLoS One 9: e90636.
23. Rogers, E.E. and Guerinot, M.L. (2002) FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. Plant Cell 14: 1787-1799.
24. Sawaki., Y., Iuchi, S., Kobayashi, Y., Kobayashi, Y., Ikka, T., Sakurai, N. et al. (2009) STOP1 regulates multiple genes which protect Arabidopsis from proton and aluminum toxicities. Plant Physiol. 150: 281-294.
25. Sharma, N., Jung, C.H., Bhalla, P.L. and Singh, M.B. (2014) RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha. PLoS One 9: e97497.
26. Shen, R. and Ma, J.F. (2001) Distribution and mobility of aluminium in an Al-accumulating plant, Fagopyrum esculentum Moench. J. Exp. Bot. 52: 1683-1687.
27. Shen., R., Ma., J.F., Kyo, M. and Iwashita, T. (2002) Compartmentation of aluminium in leaves of an Al-accumulator, Fagopyrum esculentum Moench. Planta 215: 394-398.
28. Takahashi, R., Ishimaru, Y., Senoura, T., Shimo, H., Ishikawa, S., Arao, T. et al. (2011) The OsNRAMP1 iron transporter is involved in Cd accumulation in rice. J. Exp. Bot. 62: 4843-4850.
29. Tsutsui, T., Yamaji, N., Huang, C.F., Motoyama, R., Nagamura, Y. and Ma, J.F. (2012) Comparative genome-wide transcriptional analysis of Al-responsive genes reveals novel Al tolerance mechanisms in rice. PLoS One 7: e48197.
30. Von Uexkull, H.R. and Mutert, E. (1995) Global extent, development and economic impact of acid soils. Plant Soil 171: 1-15.
31. Xia, J., Yamaji, N., Kasai, T. and Ma, J.F. (2010) Plasma membrane-localized transporter for aluminum in rice. Proc. Natl Acad. Sci. USA 107: 18381-18385.
32. Yamaji, N., Huang, C.F., Nagao, S., Yano, M., Sato, Y., Nagamura, Y. et al. (2009) A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21: 3339-3349.
33. Yokosho, K., Yamaji, N. and Ma, J.F. (2011) An Al-inducible MATE gene is involved in external detoxification of Al in rice. Plant J. 69: 1061-1069.
34. Yokosho, K., Yamaji, N., Ueno, D., Mitani, N. and Ma, J.F. (2009) OsFRDL1 is a citrate transporter required for efficient translocation of iron in rice. Plant Physiol. 149: 297-305.
35. Yu, L., Jiang, J., Zhang, C., Jiang, L., Ye, N., Lu, Y. et al. (2010) Glyoxylate rather than ascorbate is an efficient precursor for oxalate biosynthesis in rice. J. Exp. Bot. 61: 1625-1634.
36. Zhao, C.R., Ikka, T., Sawaki, Y., Kobayashi, Y., Suzuki, Y., Hibino, T. et al. (2009) Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in Arabidopsis thaliana. BMC Plant Biol. 9: 32.
37. Zheng, S.J., Ma, J.F. and Matsumoto, H. (1998) High aluminum resistance in buckwheat. I. Al-induced specific secretion of oxalic acid from root tips. Plant Physiol. 117: 745-751.