Skip to main content
SpringerLink
Log in

Genome-wide identification of SAUR genes in watermelon (Citrullus lanatus)

  • Research Article
  • Published:
Physiology and Molecular Biology of Plants Aims and scope Submit manuscript

Abstract

The early auxin responsive SAUR family is an important gene family in auxin signal transduction. We here present the first report of a genome-wide identification of SAUR genes in watermelon genome. We successfully identified 65 ClaSAURs and provide a genomic framework for future study on these genes. Phylogenetic result revealed a Cucurbitaceae-specific SAUR subfamily and contribute to understanding of the evolutionary pattern of SAUR genes in plants. Quantitative RT-PCR analysis demonstrates the existed expression of 11 randomly selected SAUR genes in watermelon tissues. ClaSAUR36 was highly expressed in fruit, for which further study might bring a new prospective for watermelon fruit development. Moreover, correlation analysis revealed the similar expression profiles of SAUR genes between watermelon and Arabidopsis during shoot organogenesis. This work gives us a new support for the conserved auxin machinery in plants.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bailey TL, Boden M, Buske FA, Frith M et al (2009) MEME SUITE: tools for motif discovery and searching. Nucl Acids Res 37:W202–W208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bao Y, Dharmawardhana P, Mockler TC, Strauss SH (2009) Genome scale transcriptome analysis of shoot organogenesis in Populus. BMC Plant Biol 9:132

    Article  PubMed  PubMed Central  Google Scholar 

  • Chae K, Isaacs CG, Reeves PH, Maloney GS et al (2012) Arabidopsis SMALL AUXIN UP RNA63 promotes hypocotyl and stamen filament elongation. Plant J 71:684–697

    Article  CAS  PubMed  Google Scholar 

  • Che P, Lall S, Nettleton D, Howell SH (2006) Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture. Plant Physiol 141:620–637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Choi PS, Soh WY, Kim YS, Yoo OJ et al (1994) Genetic transformation and plant regeneration of watermelon using Agrobacterium tumefaciens. Plant Cell Rep 13:344–348

    Article  CAS  PubMed  Google Scholar 

  • Collins JK, Wu GY, Perkins-Veazie P, Spears K et al (2007) Watermelon consumption increases plasma arginine concentrations in adults. Nutrition 23:261–266

    Article  CAS  PubMed  Google Scholar 

  • De Smet I, Voss U, Lau S, Wilson M et al (2011) Unraveling the evolution of auxin signaling. Plant Physiol 155:209–221

    Article  PubMed  Google Scholar 

  • Duclercq J, Sangwan-Norreel B, Catterou M, Sangwan RS (2011) De novo shoot organogenesis: from art to science. Trends Plant Sci 16:597–606

    Article  CAS  PubMed  Google Scholar 

  • Finet C, Jaillais Y (2012) AUXOLOGY: when auxin meets plant evo-devo. Dev Biol 369:19–31

    Article  CAS  PubMed  Google Scholar 

  • Gil P, Liu Y, Orbovic V, Verkamp E et al (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 

  • Guo SG, Liu JA, Zheng Y, Huang MY et al (2011) Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genom 12:454

    Article  CAS  Google Scholar 

  • Guo S, Zhang J, Sun H, Salse J et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58

    Article  CAS  PubMed  Google Scholar 

  • Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K et al (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 

  • Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucl Acids Res 27:297–300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang S, Li R, Zhang Z, Li L et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Chen J, Bao Y, Liu L 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 

  • Huang X, Bao Y, Wang B, Liu L et al (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(1):119–129

    Article  CAS  PubMed  Google Scholar 

  • Jain M, Tyagi AK, Khurana JP (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 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 

  • Lespinet O, Wolf YI, Koonin EV, 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 

  • Liu RX, Kuang J, Gong Q, Hou XL (2003) Principal component regression analysis with SPSS. Comput Meth Prog Biomed 71:141–147

    Article  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (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 

  • Matsui K, Hiratsu K, Koyama T, Tanaka H et al (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 BA, Hagen G, Brown CS, Gee MA et al (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 

  • Ouibrahim L, Mazier M, Estevan J, Pagny G et al (2014) Cloning of the Arabidopsis rwm1 gene for resistance to Watermelon mosaic virus points to a new function for natural virus resistance genes. Plant J 79:705–716

    Article  CAS  PubMed  Google Scholar 

  • Paponov IA, Paponov M, Teale W, Menges M et al (2008) Comprehensive transcriptome analysis of auxin responses in Arabidopsis. Mol Plant 1:321–337

    Article  CAS  PubMed  Google Scholar 

  • Pattison RJ, Csukasi F, Catalá C (2014) Mechanisms regulating auxin action during fruit development. Physiol Plant 151(1):62–72

    Article  CAS  PubMed  Google Scholar 

  • Roig-Villanova I, Bou-Torrent J, Galstyan A, Carretero-Paulet L 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 BH, 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 

  • Sato A, Sasaki S, Matsuzaki J, Yamamoto KT (2014) Light-dependent gravitropism and negative phototropism of inflorescence stems in a dominant Aux/IAA mutant of Arabidopsis thaliana, axr2. J Plant Res 127:627–639

    Article  CAS  PubMed  Google Scholar 

  • Spartz AK, Lee SH, Wenger JP, Gonzalez N 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 AK, Ren H, Park MY, Grandt KN 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, Kumar PP (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 et al (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 

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

    Article  CAS  PubMed  Google Scholar 

  • Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64:643–651

    Article  CAS  PubMed  Google Scholar 

  • Zhang N, Huang X, Bao Y, Wang B et al (2015) Genome-wide identification and expression profiling of WUSCHEL-related homeobox (WOX) genes during adventitious shoot regeneration of watermelon (Citrullus lanatus). Acta Physiol Plant 37:224

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank Dr. Adel M. R. A. Abdelaziz from Central Laboratory of Organic Agriculture, Agricultural Research Center (Giza 12619, Egypt) for manuscript revision. This study was supported by Applied Basic Research Project of Wuhan City (2015021701011611), Talent Project for Wuhan Institute of Agricultural Science (CX201615-06) and Supporting Program for Science and Technology Research of Hubei Province (2015BBA201).

Author information

Author notes

  1. Na Zhang and Xing Huang have contributed equally to this work.

Authors and Affiliations

  1. Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345, Hubei Province, China

    Na Zhang, Hongxia Zeng, Weishun Cheng, Mi Tang, Yuhua Li, Jian Ren & Yuhong Sun

  2. Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, #4 Xueyuan Road, Longhua District, Haikou, 571101, China

    Xing Huang

  3. College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China

    Yaning Bao & Bo Wang

Authors
  1. Na Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xing Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yaning Bao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bo Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hongxia Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Weishun Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Mi Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yuhua Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jian Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuhong Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuhong Sun.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, N., Huang, X., Bao, Y. et al. Genome-wide identification of SAUR genes in watermelon (Citrullus lanatus). Physiol Mol Biol Plants 23, 619–628 (2017). https://doi.org/10.1007/s12298-017-0442-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12298-017-0442-y

Keywords

Search

Navigation