Skip to main content
SpringerLink
Log in

Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea)

  • RESEARCH ARTICLE
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Small auxin-up RNA (SAUR) genes are important gene families in auxin signalling transduction and are commonly used as early auxin responsive markers. Till date, no SAUR gene is identified in Urticales plants despite of the published bioinformation of mulberry, hemp and ramie. In this study, we used Arabidopsis sequences as query to search against mulberry, hemp genomes and ramie transcriptome database. In total, we obtained 62, 56 and 71 SAUR genes in mulberry, hemp and ramie, respectively. Phylogenetic analysis revealed the Urticales specific expansion of SAUR genes. Expression analysis showed 15 randomly selected ramie SAUR genes that were diversely functioned in ramie tissues and revealed a series of IAA-responsive, drought-responsive and high temperature-responsive genes. Moreover, comparison of qRT-PCR data and previous RNA-Seq data suggested the reliability of our work. In this study, we first report the identification of SAUR genes in Urticales plants. These results will provide a foundation for their function validation in Urticales plant growth and development.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5

Similar content being viewed by others

References

  • Albert V. A., Barbazuk W. B., dePamphilis C. W., Der J. P., Leebens-Mack J., Ma H. et al. 2013 The amborella genome and the evolution of flowering plants. Sci. 342, 1467.

    Google Scholar 

  • An X., Chen J., Zhang J. Y., Liao Y. W., Dai L. J., Wang B. et al. 2015 Transcriptome profiling and identification of transcription factors in ramie (Boehmeria nivea L. Gaud) in response to PEG treatment, using illumina paired-end sequencing technology. Int. J. Mol. Sci. 16, 3493–3511.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anai T., Kono N., Kosemura S., Yamamura S. and Hasegawa K. 1998 Isolation and characterization of an auxin-inducible SAUR gene from radish seedlings. DNA seq. 9, 329–333.

    Article  CAS  PubMed  Google Scholar 

  • Bailey T. L., Boden M., Buske F. A., Frith M., Grant C. E., Clementi L. et al. 2009 MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, 202–208.

    Article  Google Scholar 

  • Barber E. J. W. 1991 Prehistoric textiles: the development of cloth in the neolithic and bronze ages with special reference to the aegean , pp. 31. Princeton University Press, Princeton, USA.

  • Bruhlmann F., Leupin M., Erismann K. H. and Fiechter A. 2000 Enzymatic degumming of ramie bast fibers. J. Biotechnol. 76, 43–50.

    Article  CAS  PubMed  Google Scholar 

  • Chae K., Isaacs C. G., Reeves P. H., Maloney G. S., Muday G. K., Nagpal P. et al. 2012 Arabidopsis SMALL AUXIN UP RNA63 promotes hypocotyl and stamen filament elongation. Plant J. 71, 684–697.

    Article  CAS  PubMed  Google Scholar 

  • Chen J., Pei Z., Dai L., Wang B., Liu L., An X. et al. 2014a Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.) BMC Genomics 15, 919.

  • Chen Y., Hao X. and Cao J. 2014b Small auxinu pregulated RNA (SAUR) gene family in maize: identification, evolution, and its phylogenetic comparison with Arabidopsis, rice, and sorghum. J. Integr. Plant Biol. 56, 133–150.

  • Franklin K. A., Lee S. H., Patel D., Kumar S. V., Spartz A. K., Gu C. et al. 2011 PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature. Proc. Nat. Acad. Sci. USA 108, 20231–20235.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gil P., Liu Y., Orbovic V., Verkamp E., Poff K. L. and Green P. J. 1994 Characterization of the auxin-inducible SAUR-AC1 gene for use as a molecular genetic tool in Arabidopsis. Plant Physiol. 104, 777–784.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hanada K., Zou C., Lehti-Shiu M. D., Shiu S. H and Shinozaki K. 2008 Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148, 993–1003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He N., Zhang C., Qi X., Zhao S., Tao Y., Yang G. et al. 2013 Draft genome sequence of the mulberry tree Morus notabilis . Nat. Commun. 4, 2445.

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang X., Chen J., Bao Y., Liu L., Jiang H., An X. et al. 2014 Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of ramie (Boehmeria nivea L. Gaud). PLoS One 9, e113768.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jaillon O., Aury J. M. and Wincker P. 2009 “Changing by doubling”, the impact of whole genome duplications in the evolution of eukaryotes. C. R. Biol. 332, 241–253.

    Article  CAS  PubMed  Google Scholar 

  • Jain M. and Khurana J. P. 2009 Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J. 276, 3148–3162.

    Article  CAS  PubMed  Google Scholar 

  • Jain M., Tyagi A. K. and Khurana J. P. 2006 Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics 88, 360–371.

    Article  CAS  PubMed  Google Scholar 

  • Kong Q., Yuan J., Gao L., Zhao S., Jiang W., Huang Y. et al. 2014 Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon. PLoS One 9, e90612.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuang J. F., Wu J. Y., Zhong H. Y., Li C. Q., Chen J. Y., Lu W. J. et al. 2012 Carbohydrate stress affecting fruitlet abscission and expression of genes related to auxin signal transduction pathway in litchi. Int. J. Mol. Sci. 13, 16084–16103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lehti-Shiu M. D., Zou C., Hanada K. and Shiu S. H. 2009 Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol. 150, 12–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lespinet O., Wolf Y. I., Koonin E. V. and Aravind L. 2002 The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12, 1048–1059.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H. L. 1974 An archaeological and historical account of cannabis in China. Economic Bot. 28, 437–448.

    Article  Google Scholar 

  • Licciardello C., Torrisi B., Allegra M., Sciacca F., Roccuzzo G., Intrigliolo F. et al. 2013 A transcriptomic analysis of sensitive and tolerant citrus rootstocks under natural iron deficiency conditions. J. Am. Soc. Hort. Sci. 138, 487–498.

    CAS  Google Scholar 

  • Livak K. J. and Schmittgen T. D. 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25, 402–408.

    Article  CAS  PubMed  Google Scholar 

  • Marois E., Van den Ackerveken G. and Bonas U. 2002 The xanthomonas type III effector protein AvrBs3 modulates plant gene expression and induces cell hypertrophy in the susceptible host. Mol. Plant Microbe Interact. 15, 637–646.

    Article  CAS  PubMed  Google Scholar 

  • Matsui K., Hiratsu K., Koyama T., Tanaka H. and Ohme-Takagi M. 2005 A chimeric AtMYB23 repressor induces hairy roots, elongation of leaves and stems, and inhibition of the deposition of mucilage on seed coats in Arabidopsis. Plant Cell Physiol. 46, 147–155.

    Article  CAS  PubMed  Google Scholar 

  • McClure B. A., Hagen G., Brown C. S., Gee M. A. and Guilfoyle T. J. 1989 Transcription, organization, and sequence of an auxin-regulated gene cluster in soybean. Plant cell 1, 229–239.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qiu T., Chen Y., Li M., Kong Y., Zhu Y., Han N. et al. 2013 The tissue-specific and developmentally regulated expressionpatterns of the SAUR41 subfamily of small auxin up RNA genes: potential implications. Plant Signal. Behav. 8, e25283.

    Article  PubMed  PubMed Central  Google Scholar 

  • Roig-Villanova I., Bou-Torrent J., Galstyan A., Carretero-Paulet L., Portoles S., Rodriguez-Concepcion M. et al. 2007 Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins. EMBO J. 26, 4756–4767.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roux C., Bilang J., Theunissen B. H. and Perrot-Rechenmann C. 1998 Identification of new early auxin markers in tobacco by mRNA differential display. Plant Mol. Biol. 37, 385–389.

    Article  CAS  PubMed  Google Scholar 

  • Spartz A. K., Lee S. H., Wenger J. P., Gonzalez N., Itoh H., Inze D. et al. 2012 The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion. Plant J. 70, 978–990.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spartz A. K., Ren H., Park M. Y., Grandt K. N., Lee S. H., Murphy A. S. et al. 2014 SAUR Inhibition of PP2C-D phosphatases activates plasma membrane H + -ATPases to promote cell expansion in arabidopsis. Plant Cell 26, 2129–2142.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamm P. and Kumar P. P. 2013 Auxin and gibberellin responsive Arabidopsis SMALL AUXIN UP RNA36 regulates hypocotyl elongation in the light. Plant Cell Rep. 32, 759–769.

    Article  CAS  PubMed  Google Scholar 

  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tatsuki M., Nakajima N., Fujii H., Shimada T., Nakano M., Hayashi K. et al. 2013 Increased levels of IAA are required for system 2 ethylene synthesis causing fruit softening in peach (Prunus persica L. Batsch). J. Exp. Bot. 64, 1049–1059.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F. and Higgins D. G. 1997 The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Bakel H., Stout J. M., Cote A. G., Tallon C. M., Sharpe A. G., Hughes T. R. et al. 2011 The draft genome and transcriptome of Cannabis sativa. Genome Biol. 12, R102.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watillon B., Kettmann R., Arredouani A., Hecquet J. F., Boxus P. and Burny A. 1998 Apple messenger RNAs related to bacterial lignostilbene dioxygenase and plant SAUR genes are preferentially expressed in flowers. Plant Mol. Biol. 36, 909– 915.

    Article  CAS  PubMed  Google Scholar 

  • Wu J., Liu S., He Y., Guan X., Zhu X., Cheng L. et al. 2012 Genome-wide analysis of SAUR gene family in Solanaceae species. Gene 509, 38–50.

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto K. T. 1994 Further characterization of auxin-regulated mRNAs in hypocotyl sections of mung bean [Vigna radiata (L.) Wilczek]: sequence homology to genes for fatty-acid desaturases and atypical late-embryogenesis-abundant protein, and the mode of expression of the mRNAs. Planta 192, 359–364.

    Article  CAS  PubMed  Google Scholar 

  • Yang T. and Poovaiah B. W. 2000 Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action. J. Biol. Chem. 275, 3137–3143.

    Article  CAS  PubMed  Google Scholar 

  • Yang X., Zhang X., Yuan D., Jin F., Zhang Y. and Xu J. 2012 Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC Plant Biol. 12, 110.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zurek D. M., Rayle D. L, McMorris T. C. and Clouse S. D. 1994 Investigation of gene expression, growth kinetics, and wall extensibility during brassinosteroid-regulated stem elongation. Plant Physiol. 104, 505–513.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This study was supported by the National Natural Science Funds (31171594), the Fundamental Research Funds for the Central Universities (2662015PY059) and China Agriculture Research System (CARS-19-E12).

Author information

Authors and Affiliations

  1. MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Road, Wuhan, 430070, People’s Republic of China

    XING HUANG, YANING BAO, BO WANG, LIJUN LIU, JIE CHEN, LUNJIN DAI, SANA ULLAH BALOCH & DINGXIANG PENG

Authors
  1. XING HUANG
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. YANING BAO
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. BO WANG
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. LIJUN LIU
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. JIE CHEN
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. LUNJIN DAI
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. SANA ULLAH BALOCH
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. DINGXIANG PENG
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to DINGXIANG PENG.

Additional information

[Huang X., Bao Y., Wang B., Liu L., Chen J., Dai L., Baloch S. U. and Peng D. 2016. Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea). J. Genet. 95, xx–xx]

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

HUANG, X., BAO, Y., WANG, B. et al. Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea). J Genet 95, 119–129 (2016). https://doi.org/10.1007/s12041-016-0622-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-016-0622-5

Keywords

Search

Navigation