, Volume 246, Issue 1, pp 91–103 | Cite as

An RNA-Seq transcriptome analysis revealing novel insights into aluminum tolerance and accumulation in tea plant

  • Yong Li
  • Jie Huang
  • Xiaowei Song
  • Ziwei Zhang
  • Ye Jiang
  • Yulu Zhu
  • Hua ZhaoEmail author
  • Dejiang Ni
Original Article


Main conclusion

The tea plant ( Camellia sinensis L. O. Kuntze) is a high aluminum (Al) tolerant and accumulator species. Candidate genes related to Al tolerance in tea plants were assembled based on de novo transcriptome analysis. The homologs implied some common and distinct Al-tolerant mechanism between tea plants and rice, Arabidopsis and buckwheat.

In addition to high Al tolerance, the tea plant exhibits good performance exposure to a proper Al level, and accumulates high Al in the leaves without any toxicity symptom. Therefore, Al was considered as a hyperaccumulator and beneficial element for tea plants. However, the whole-genome molecular mechanisms accounting for Al-tolerance and accumulation remain unknown in tea plants. In this study, transcriptome analysis by RNA-Seq following a gradient Al-level exposure was assessed to further reveal candidate genes involved. Totally more than 468 million high-quality reads were generated and 213,699 unigenes were de novo assembled, among which 8922 unigenes were all annotated in the seven databases used. A large number of transporters, transcription factors, cytochrome P450, ubiquitin ligase, organic acid biosynthesis, heat shock proteins differentially expressed in response to high Al (P ≤ 0.05) were identified, which were most likely ideal candidates involved in the Al tolerance or accumulation. Furthermore, a few of the candidate Al-responsive genes related to Al sequestration, cell wall modification and organic acid excretion have been well elucidated as was already found in Arabidopsis, rice, and buckwheat. Thus, some consistent Al-tolerance mechanisms across the species are indicated. In conclusion, the transcriptome data provided useful insights of promising candidates for further characterizing the functions of genes involved in Al tolerance and accumulation in tea plants.


Aluminum stress Candidate genes De novo transcriptome Camellia sinensis L.O. Kuntze 



Aluminum-activated malate transporter


Aluminum resistance transcription factor 1


Differentially expressed genes


Glutathione-S transferase 1


Multidrug and toxic compound extrusion

STAR1, 2

Sensitive to aluminum rhizotoxicity 1, 2


Sensitive to proton rhizotoxicity 1



This work was jointly supported by National Natural Science Foundation of China (31470406), the Fundamental Research Funds for the Central Universities (2662015BQ011, 2016BC001) and National Undergraduate Training Programs for Innovation and Entrepreneurship (201510504033).

Supplementary material

425_2017_2688_MOESM1_ESM.docx (794 kb)
Supplementary material 1 (DOCX 794 kb)


  1. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:1–12CrossRefGoogle Scholar
  2. Barceló J, Poschenrieder C (2002) Fast root growth responses, root exudates, and internal detoxification as clues to the mechanisms of aluminium toxicity and resistance: a review. Environ Exp Bot 48:75–92CrossRefGoogle Scholar
  3. Chen S, Tao L, Zeng L, Vega-Sanchez ME, Umemura K, Wang GL (2006) A highly efficient transient protoplast system for analyzing defence gene expression and protein-protein interactions in rice. Mol Plant Pathol 7:417–427CrossRefPubMedGoogle Scholar
  4. Chen ZC, Yamaji N, Motoyama R (2012) Up-regulation of a magnesium transporter gene OsMGT1 is required for conferring aluminum tolerance in rice. Plant Physiol 159:1624–1633CrossRefPubMedPubMedCentralGoogle Scholar
  5. Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV (2010) Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms. Plant Physiol 153:1678–1691CrossRefPubMedPubMedCentralGoogle Scholar
  6. Foy CD (1988) Plant adaptation to acid, aluminum-toxic soils. Commun Soil Sci Plant Anal 19:959–987CrossRefGoogle Scholar
  7. Furukawa J, Yamaji N, Wang H (2007) An aluminum activated citrate transporter in barley. Plant Cell Physiol 48:1081–1091CrossRefPubMedGoogle Scholar
  8. Gao HJ, Zhao Q, Zhang XC (2014) Localization of fluoride and aluminum in subcellular fractions of tea leaves and roots. J Agric Food Chem 62:2313–2319CrossRefPubMedGoogle Scholar
  9. Götz S, Garcíagómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435CrossRefPubMedPubMedCentralGoogle Scholar
  10. Guo JH, Liu XJ, Zhang Y, Shen JL, Han WX, Zhang WF, Christie P, Goulding KW, Vitousek PM, Zhang FS (2010) Significant acidification in major Chinese croplands. Science 327:1008–1010CrossRefPubMedGoogle Scholar
  11. Hajiboland R, Barceló J, Poschenrieder C, Tolrà R (2013) Amelioration of iron toxicity: a mechanism for aluminum-induced growth stimulation in tea plants. J Inorg Biochem 128:183–187CrossRefPubMedGoogle Scholar
  12. Hellmann H, Estelle M (2002) Plant development: Regulation by protein degradation. Science 297:793–797CrossRefPubMedGoogle Scholar
  13. Horst WJ, Wang Y, Eticha D (2010) The role of the root apoplast in aluminium induced inhibition of root elongation and in aluminium resistance of plants: a review. Ann Bot 106:185–197CrossRefPubMedPubMedCentralGoogle Scholar
  14. Huang CF, Yamaji N, Mitani N (2009) A bacterial-type ABC transporter is involved in aluminum tolerance in rice. Plant Cell 21:655–667CrossRefPubMedPubMedCentralGoogle Scholar
  15. Huang CF, Yamaji N, Ma JF (2010) Knockout of a bacterial-type ATP-binding cassette transporter gene, AtSTAR1, results in increased aluminum sensitivity in Arabidopsis. Plant Physiol 153:1669–1677CrossRefPubMedPubMedCentralGoogle Scholar
  16. Huang CF, Yamaji N, Chen Z, Ma JF (2012) A tonoplast-localized half-size ABC transporter is required for internal detoxification of aluminum in rice. Plant J Cell Mol Biol 69:857–867CrossRefGoogle Scholar
  17. Iuchi S, Koyama H, Iuchi A, Kobayashi Y, Kitabayashi S, Ikka T, Hirayama T, Shinozaki K, Kobayashi M (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 104:9900–9905CrossRefPubMedPubMedCentralGoogle Scholar
  18. Jack DL, Yang NM, July Saier MH (2001) The drug/metabolite transporter superfamily. Eur J Biochem 268(13):3620–3639CrossRefPubMedGoogle Scholar
  19. Kumari M, Taylor GJ, Deyholos MK (2008) Transcriptomic responses to aluminum stress in roots of Arabidopsis thaliana. Mol Genet Genom 279:339–357CrossRefGoogle Scholar
  20. Larsen PB, Geisler MJ, Jones CA, Williams KM, Cancel JD (2005) ALS3 encodes a phloem-localized ABC transporter-like protein that is required for aluminum tolerance in Arabidopsis. Plant J 41:353–363CrossRefPubMedGoogle Scholar
  21. Li B, Dewey C (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:93–99CrossRefGoogle Scholar
  22. Li XF, Ma JF, Matsumoto H (2000) Pattern of aluminum-induced secretion of organic acids differs between rye and wheat. Plant Physiol 123:1537–1544CrossRefPubMedPubMedCentralGoogle Scholar
  23. Liu LH, Wirén NV (2003) Urea transport by nitrogen-regulated tonoplast intrinsic proteins in Arabidopsis. Plant Physiol 133:1220–1228CrossRefPubMedPubMedCentralGoogle Scholar
  24. Liu JP, Magalhaes JV, Shaff J, Kochian LV (2009) Aluminum activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance. Plant J 57:389–399CrossRefPubMedGoogle Scholar
  25. Loqué D, Ludewig U, Yuan L, Von WN (2005) Tonoplast intrinsic proteins AtTIP2;1 and AtTIP2;3 facilitate NH3 transport into the vacuole. Plant Physiol 137:671–680CrossRefPubMedPubMedCentralGoogle Scholar
  26. Ma JF, Hiradate S, Nomoto K, Iwashita T, Matsumoto H (1997) Internal detoxification mechanism of Al in hydrangea (identification of Al form in the leaves). Plant Physiol 113:1033–1039CrossRefPubMedPubMedCentralGoogle Scholar
  27. Ma JF, Hiradate S, Matsumoto H (1998) High aluminum resistance in buckwheat-II. Oxalic acid detoxifies aluminum internally. Plant Physiol 117:753–759CrossRefPubMedCentralGoogle Scholar
  28. Ma JF, Shen R, Zhao Z, Wissuwa M, Takeuchi Y (2002) Response of rice to Al stress and identification of quantitative trait loci for Al tolerance. Plant Cell Physiol 43:652–659CrossRefPubMedGoogle Scholar
  29. Magalhaes JV, Liu J, Guimaraes CT (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39:1156–1161CrossRefPubMedGoogle Scholar
  30. Maron LG, Pineros MA, Guimaraes CT, Magalhaes JV, Pleiman JK, Mao CZ, Shaff J, Belicuas SNJ, Kochian LV (2010) Two functionally distinct members of the MATE (multi-drug and toxic compound extrusion) family of transporters potentially underlie two major aluminum tolerance QTLs in maize. Plant J 61:728–740CrossRefPubMedGoogle Scholar
  31. Matsumoto H (2000) Cell biology of aluminium toxicity and tolerance in higher plants. Int Rev Cytol 200:1–46CrossRefPubMedGoogle Scholar
  32. Matsumoto H, Hirasawa E, Morimura S, Takahashi E (1976) Localization of aluminium in tea leaves. Plant Cell Physiol 17:627–631CrossRefGoogle Scholar
  33. Moon J, Parry G, Estelle M (2004) The ubiquitin-proteasome pathway and plant development. Plant Cell 16:3181–3195CrossRefPubMedPubMedCentralGoogle Scholar
  34. Morita A, Horie H, Fujii Y, Takatsu S, Wtanabe N, Yagia A, Yokotaa H (2004) Chemical forms of aluminum in xylem sap of tea plants (Camellia sinensis L.). Phytochemistry 65:2775–2780CrossRefPubMedGoogle Scholar
  35. Morita A, Yanagisawa O, Takatsu S, Maeda S, Hiradate S (2008) Mechanism for the detoxification of aluminum in roots of tea plant [Camellia sinensis (L.) Kuntze]. Phytochemistry 69:147–153CrossRefPubMedGoogle Scholar
  36. Morita A, Yanagisawa O, Maeda S, Takatsu S, Ikka T (2011) Tea plant (Camellia sinensis L.) roots secrete oxalic acid and caffeine into medium containing aluminum. Soil Sci Plant Nutr 57:796–802CrossRefGoogle Scholar
  37. Nagata T, Hayatsu M, Kosuge N (1991) Direct observation of aluminum in plants by nuclear magnetic resonance. Anal Sci 7:213–215CrossRefGoogle Scholar
  38. Nagata T, Hayatsu M, Kosuge N (1992) Identification of aluminium forms in tea leaves by 27Al NMR. Phytochemistry 31:1215–1218CrossRefGoogle Scholar
  39. Naumann A, Horst WJ (2003) Effect of aluminium supply on aluminium uptake, translocation and blueing of Hydrangea macrophylla (Thunb.) Ser. cultivars in a peat-clay substrate. J Hortic Sci Biotechnol 78:463–469CrossRefGoogle Scholar
  40. Negishi T, Oshima K, Hattori M, Kanai M, Mano S, Nishimura M, Yoshida K (2012) Tonoplast- and plasma membrane-localized aquaporin-family transporters in blue hydrangea sepals of aluminum hyperaccumulating plant. PLoS One 7:e43189CrossRefPubMedPubMedCentralGoogle Scholar
  41. Oh MW, Roy SK, Kamal AHM, Cho K, Cho SW, Park CS, Choi JS, Komatsu S, Woo SH (2014) Proteome analysis of roots of wheat seedlings under aluminum stress. Mol Biol Rep 41:671–681CrossRefPubMedGoogle Scholar
  42. Ohyama Y, Ito H, Kobayashi Y, Ikka T, Morita A, Kobayashi M, Imaizumi R, Aoki T, Komatsu K, Sakata Y, Iuchi S, Koyama H (2013) Characterization of AtSTOP1 orthologous genes in tobacco and other plant species. Plant Physiol 162:1937–1946CrossRefPubMedPubMedCentralGoogle Scholar
  43. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ (2008) A large genome center’s improvements to the Illumina sequencing system. Nat Methods 5:1005–1010CrossRefPubMedPubMedCentralGoogle Scholar
  44. Režen T, Debeljak N, Kordiš D, Rozman D (2004) New aspects on lanosterol 14α-demethylase and cytochrome P450 evolution: lanosterol/cycloartenol diversification and lateral transfer. J Mol Evol 59:51–58CrossRefPubMedGoogle Scholar
  45. Richards KD, Schott EJ, Sharma YK, Davis KR, Gardner RC (1998) Aluminum induces oxidative stress genes in Arabidopsis thaliana. Plant Physiol 116:409–418CrossRefPubMedPubMedCentralGoogle Scholar
  46. Sasaki T, Yamamoto Y, Ezaki B, Katsuhara M, Ahn SJ, Ryan PR, Delhaize E, Matsumoto H (2004) A wheat gene encoding an aluminum-activated malate transporter. Plant J 37:645–653CrossRefPubMedGoogle Scholar
  47. Sawaki Y, Iuchi S, Kobayashi Y, Kobayashi Y, Ikka T, Sakurai N, Fujita M, Shinozaki K, Shibata D, Kobayashi M, Koyama H (2009) STOP1 regulates multiple genes that protect Arabidopsis from proton and aluminum toxicities. Plant Physiol 150:281–294CrossRefPubMedPubMedCentralGoogle Scholar
  48. Shaff JE, Schultz BA, Craft EJ, Clark RT, Kochian LV (2010) GEOCHEM-EZ: a chemical speciation program with greater power and flexibility. Plant Soil 330:207–214CrossRefGoogle Scholar
  49. Taylor GJ (1991) Current views of the aluminum stress response: the physiological basis of tolerance. Curr Topics Plant Biochem Physiol 10:57–93Google Scholar
  50. Tolrà R, Vogel-Mikuš K, Hajiboland R, Kump P, Pongrac P, Kaulich B, Gianoncelli A, Babin V, Barceló J, Regvar M, Poschenrieder C (2011) Localization of aluminium in tea (Camellia sinensis) leaves using low energy X-ray fluorescence spectro-microscopy. J Plant Res 124:165–172CrossRefPubMedGoogle Scholar
  51. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515CrossRefPubMedPubMedCentralGoogle Scholar
  52. Uexküll HR, Mutert E (1995) Global extent, development and economic impact of acid soils. Plant Soil 171:1–15CrossRefGoogle Scholar
  53. Wagatsuma T, Khan MSH, Watanabe T, Maejima E, Sekimoto H, Yokota T, Nakano T, Toyomasu T, Tawaraya K, Koyama H, Uemura M, Ishikawa S, Ikka T, Ishikawa A, Kawamura T, Murakami S, Ueki N, Umetsu A, Kannari T (2015) Higher sterol content regulated by CYP51 with concomitant lower phospholipid content in membranes is a common strategy for aluminium tolerance in several plant species. J Exp Bot 66:907–918CrossRefPubMedGoogle Scholar
  54. Watanabe T, Osaki M (2002) Mechanism of adaptation to high aluminium condition in native plant species growing in acid soils: a review. Commun Soil Sci Plant Anal 33:1247–1260CrossRefGoogle Scholar
  55. Xia J, Yamaji N, Kasai T (2010) Plasma membrane-localized transporter for aluminum in rice. Proc Natl Acad Sci USA 107:18381–18385CrossRefPubMedPubMedCentralGoogle Scholar
  56. Yamaji N, Huang CF, Nagao S (2009) A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21:3339–3349CrossRefPubMedPubMedCentralGoogle Scholar
  57. Yokosho K, Yamaji N, Ma JF (2011) An Al-inducible MATE gene is involved in external detoxification of Al in rice. Plant J 68:1061–1069CrossRefPubMedGoogle Scholar
  58. Yokosho K, Yamaji N, Ma JF (2014) Global transcriptome analysis of Al-induced genes in an Alaccumulating species, common buckwheat (Fagopyrum esculentum Moench). Plant Cell Physiol 55(12):2077–2091CrossRefPubMedGoogle Scholar
  59. Yoshida Y, Aoyama Y, Noshiro M, Gotoh O (2000) Sterol 14-demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily. Biochem Biophys Res Commun 273:799–804CrossRefPubMedGoogle Scholar
  60. Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14CrossRefPubMedPubMedCentralGoogle Scholar
  61. Zhang YY, Xie Q (2007) Ubiquitination in abscisic acid-related pathway. J Integr Plant Biol 49(1): 87–93CrossRefGoogle Scholar
  62. Zhu YZ, Han YF, Zhao HS, Li J, Hu CW, Li YF, Zhang ZG (2013) Suppressive effect of accumulated aluminum trichloride on the hepatic microsomal cytochrome P450 enzyme system in rats. Food Chem Toxicol 51:210–214CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Yong Li
    • 1
    • 2
  • Jie Huang
    • 1
    • 2
  • Xiaowei Song
    • 1
    • 2
  • Ziwei Zhang
    • 1
    • 2
  • Ye Jiang
    • 1
    • 2
  • Yulu Zhu
    • 1
    • 2
  • Hua Zhao
    • 1
    • 2
    Email author
  • Dejiang Ni
    • 1
    • 2
  1. 1.Key Laboratory of Horticultural Plant Biology of Ministry of EducationHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  2. 2.College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanPeople’s Republic of China

Personalised recommendations