Molecular Biology Reports

, Volume 46, Issue 2, pp 1625–1634 | Cite as

The roles of Aux/IAA gene family in development of Dendrocalamus sinicus (Poaceae: Bambusoideae) inferred by comprehensive analysis and expression profiling

  • Lingna Chen
  • Xianggan Zheng
  • Xiaojuan Guo
  • Yongzhong Cui
  • Hanqi YangEmail author
Original Article


Auxin is an important hormone in many plant developmental processes. In this study, the auxin/indole acetic acid (Aux/IAA) gene family was comprehensively identified using Dendrocalamus sinicus transcriptome data. A total of 26 Aux/IAA genes (DsIAA1DsIAA26) were mined using four conserved Aux/IAA family motifs (PF02309). They encoded hydrophilic proteins, including one or two nuclear localisation signals. The D. sinicus Aux/IAA proteins were classified into two groups, including seven sister-gene pairs based on their phylogenetic relationships. A phylogenetic tree generated by aligning 108 predicted protein sequences of 26 DsIAAs, 43 PhIAAs (Phyllostachys heterocycla), 29 AtIAAs (Arabidopsis), 31 OsIAAs (Oryza sativa) and 22 PtIAAs (Populus) revealed nine major groups. Among them, four groups, including 96 IAA proteins of all five species, suggested that the genes originated before divergence of monocots and dicots. The expression profiling in different tissues showed that most of the DsIAAs preferentially expressed in leaves and shoots, suggesting their important roles in the development of leaves and shoots in D. sinicus. Continuously high expression of DsIAA3, DsIAA4, DsIAA15, and DsIAA20 may be important for regulating shoot development in D. sinicus. These results provide useful information for further research into the function of Aux/IAA genes in woody sympodial bamboos.


Dendrocalamus sinicus Auxin Aux/IAA gene family Bioinformatics analysis Expression profiling 



This research was funded by the Fundamental Research Funds of the Chinese Academy of Forestry (Grant Nos. CAFYBB2017ZX001-8, CAFYBB2017QA014), the National Natural Science Foundation of China (Grant Nos. 31800503; 31870574), Department of Sciences and Technology of Yunnan Province (Grant No. 2014HB041).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Research involving human and animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (DOCX 1008 KB)
11033_2019_4611_MOESM2_ESM.docx (17 kb)
Supplementary material 2 (DOCX 16 KB)
11033_2019_4611_MOESM3_ESM.docx (18 kb)
Supplementary material 3 (DOCX 18 KB)


  1. 1.
    Wang Y, Deng D, Bian Y, Lv Y, Xie Q (2010) Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.). Mol Biol Rep 37:3991–4001. CrossRefPubMedGoogle Scholar
  2. 2.
    Çakir B, Kiliçkaya O, Olcay AC (2013) Genome-wide analysis of Aux/IAA, genes in Vitis vinifera: cloning and expression profiling of a grape Aux/IAA, gene in response to phytohormone and abiotic stresses. Acta Physiol Plant 35:365–377. CrossRefGoogle Scholar
  3. 3.
    Sghaier N, Ayed RB, Gorai M, Rebai A (2018) Prediction of auxin response elements based on data fusion in Arabidopsis thaliana. Mol Biol Rep. CrossRefPubMedGoogle Scholar
  4. 4.
    Quint M, Gray WM (2006) Auxin signaling. Curr Opin Plant Biol 9:448–453. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Kalluri UC, Difazio SP, Brunner AM, Tuskan GA (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 7:59. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Uberti-Manassero NG, Lucero LE, Viola IL, Vegetti AC, Gonzalez DH (2012) The class I protein AtTCP15 modulates plant development through a pathway that overlaps with the one affected by CIN-like TCP proteins. J Exp Bot 63:809–823. CrossRefPubMedGoogle Scholar
  7. 7.
    Song Y, Xu ZF (2013) Ectopic overexpression of an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) gene OsIAA4 in rice induces morphological changes and reduces responsiveness to auxin. Int J Mol Sci 14:13645–13656. CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Yu H, Soler M, Clemente HS, Mila I, Paiva JA, Myburg AA, Bouzayen M, Grima-Pettenati J, Cassan-Wang H (2015) Comprehensive genome-wide analysis of the Aux/IAA gene family in Eucalyptus: evidence for the role of EgrIAA4 in wood formation. Plant Cell Physiol 56:700. CrossRefPubMedGoogle Scholar
  9. 9.
    Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49:387. CrossRefPubMedGoogle Scholar
  10. 10.
    Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006) Structure and early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genom 6:47–59. CrossRefGoogle Scholar
  11. 11.
    Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z (2015) A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.). Front Plant Sci 6:770. CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Nemhauser JL (2018) Back to basics: what is the function of an Aux/IAA in auxin response? New Phytol 218:1295–1297. CrossRefPubMedGoogle Scholar
  13. 13.
    Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker JR, Kay SA, Pruneda-Paz J, Estelle M (2017) Plant stress tolerance requires auxin-sensitive Aux/IAA transcriptional repressors. Curr Biol 27:437–444. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Bhandawat A, Singh G, Seth R, Singh P, Sharma RK (2017) Genome-wide transcriptional profiling to elucidate key candidates involved in bud burst and rattling growth in a subtropical bamboo (Dendrocalamus hamiltonii). Front Plant Sci 7:2038. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Zhao H, Wang L, Dong L, Sun H, Gao Z (2014) Discovery and comparative profiling of microRNAs in representative monopodial bamboo (Phyllostachys edulis) and sympodial bamboo (Dendrocalamus latiflorus). PLoS ONE 9:e102375. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Cui K, He CY, Zhang JG, Duan AG, Zeng YF (2012) Temporal and spatial profiling of internode elongation-associated protein expression in rapidly growing culms of bamboo. J Proteome Res 11:2492–2507. CrossRefPubMedGoogle Scholar
  17. 17.
    He CY, Cui K, Zhang JG, Duan AG, Zeng YF (2013) Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in moso bamboo. BMC Plant Biol 13:119. CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Peng Z, Zhang C, Zhang Y, Hu T, Mu S, Li X, Gao J (2013) Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis). PLoS ONE 8:e78944. CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Wang W, Gu L, Ye S, Zhang H, Cai C, Xiang M, Gao Y, Wang Q, Lin C, Zhu Q (2017) Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla). BMC Genom 18:870. CrossRefGoogle Scholar
  20. 20.
    Li L, Cheng Z, Ma Y, Bai Q, Li X, Cao Z, Wu Z, Gao J (2017) The association of hormone signaling genes, transcription, and changes in shoot anatomy during moso bamboo growth. Plant Biotech J 16:72–85. CrossRefGoogle Scholar
  21. 21.
    Geng BJ, Wang ZP (1996) Gramineae Bambusiodeae. In: Flora reipublicae popularis sinica, Vol 9. Science Press, Beijing, pp. 3–16Google Scholar
  22. 22.
    Hong DY, Blackmore S (2005) Plants of China. In: A companion to the flora of China. Science Press, Beijing, pp. 319–320Google Scholar
  23. 23.
    Hui CM, Yang XY, Liang N, Chen F (2014) A study on the conservation and development of Dendrocalamus sinicus form Yunnan, China. Appl Mech Mater 522–524:1084–1088. CrossRefGoogle Scholar
  24. 24.
    Chen L, Guo X, Cui Y, Zheng X, Yang H (2018) Comparative transcriptome analysis reveals hormone signaling genes involved in the launch of culm-shape differentiation in Dendrocalamus sinicus. Genes 9:4. CrossRefGoogle Scholar
  25. 25.
    Keeling CI, Weisshaar S, Ralph SG, Jancsik S, Hamberger B, Dullat HK, Bohlmann J (2011) Transcriptome mining, functional characterization, and phylogeny of a large terpene synthase gene family in spruce (Picea spp.). BMC Plant Biol 11:43. CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870. CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2–△△Ct method. Methods 25:402–408. CrossRefGoogle Scholar
  29. 29.
    Gui YJ, Zhou Y, Wang Y, Wang S, Wang SY, Hu Y, Bo SP, Chen H, Zhou CP, Ma NX, Zhang TZ, Fan LJ (2010) Insights into the bamboo genome: syntenic relationships to rice and sorghum. J Integr Plant Biol 52:1008–1015. CrossRefPubMedGoogle Scholar
  30. 30.
    Bai Q, Hou D, Li L, Cheng Z, Ge W, Liu J, Li X, Mu S, Gao J (2016) Genome-wide analysis and expression characteristics of small auxin-up RNA (SAUR) genes in moso bamboo (Phyllostachys edulis). Genome 60:325. CrossRefPubMedGoogle Scholar
  31. 31.
    Liu H, Min W, Zhu D, Feng P, Wang Y, Wang Y, Xiang Y (2017) Genome-wide analysis of the AAAP gene family in moso bamboo (Phyllostachys edulis). BMC Plant Biol 17:29. CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Li L, Mu S, Cheng Z, Cheng Y, Zhang Y, Miao Y, Hou C, Li X, Gao J (2017) Characterization and expression analysis of the WRKY gene family in moso bamboo. Sci Rep 7:6675. CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Cui K, Wang H, Liao S, Tang Q, Li L, Cui Y, He Y (2016) Transcriptome sequencing and analysis for culm elongation of the world’s largest bamboo (Dendrocalamus sinicus). PLoS ONE 11:e0157362. CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Chen Y, Cao Y, Hu S, Huang Y, Lu X, Xu G, Long Z (2016) Transcriptome analysis and gene function annotation of Bambusa emeiensis shoots based on high-throughput sequencing technology. Chin J Biotech 32:1610–1623. CrossRefGoogle Scholar
  35. 35.
    Li H, Tiwari SB, Hagen G, Guilfoyle TJ (2011) Identical amino acid substitutions in the repression domain of auxin/indole-3-acetic acid proteins have contrasting effects on auxin signaling. Plant Physiol 155:1252. CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Audran-Delalande C, Bassa C, Mila I, Regad F, Zouine M, Bouzayen M (2012) Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiol 53:659. CrossRefPubMedGoogle Scholar
  37. 37.
    Tao S, Estelle M (2018) Mutational studies of the Aux/IAA proteins in Physcomitrella reveal novel insights into their function. New Phytol 218:1534–1542. CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Sato A, Yamamoto KT (2008) Overexpression of the non-canonical Aux/IAA genes causes auxin-related aberrant phenotypes in Arabidopsis. Physiol Plant 133:397–405. CrossRefPubMedGoogle Scholar
  39. 39.
    Wu J, Peng Z, Liu S, He Y, Cheng L, Kong F, Wang J, Lu G (2012) Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a model. Mol Genet Genomics 287:295. CrossRefPubMedGoogle Scholar
  40. 40.
    Zuo X, Xu T, Qi M, Lv S, Li J, Gao S, Li T (2012) Expression patterns of auxin-responsive genes during tomato flower pedicel abscission and potential effects of calcium. Aust J Bot 60:68–78. CrossRefGoogle Scholar
  41. 41.
    Paponov IA, Teale W, Lang D, Paponov M, Reski R, Rensing SA, Palme K (2009) The evolution of nuclear auxin signalling. BMC Evol Biol 9:126. CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Luo J, Zhou JJ, Zhang JZ (2018) Aux/IAA gene family in plants: molecular structure, regulation, and function. Int J Mol Sci 19:259. CrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Research Institute of Resources InsectsChinese Academy of ForestryBailongsi, KunmingChina

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