Advertisement

Russian Journal of Plant Physiology

, Volume 65, Issue 4, pp 604–610 | Cite as

Identification of Genes Related to Cell Wall Metabolism and Fruit Ripening in Ziziphus jujube Using RNA-seq and Expression Analysis

Research Papers
  • 4 Downloads

Abstract

The transcriptome of Chinese jujube (Ziziphus jujube Mill.) fruit was characterized to determine which genes were involved in cell wall metabolism and ripening. Based on RNA-seq of fruit pulp, 61.243 contigs (mean length 440 nt) were assembled and 31.725 genes were identified (mean length 842 nt), of which 25.257 were annotated using a non-redundant protein sequence database (Nr). Finally, 8.409 of these genes were classified using the Gene Ontology (GO) functional annotation database into three major categories: cell component, molecular function, and biology process. Comparison of young and mature fruit transcripts showed that 1.206 genes were upregulated while 1.256 genes were downregulated. The 19 candidate genes related to cell wall metabolism and fruit ripening were selected from the differentially expressed genes (DEGs) for further study; qRT-PCR analysis showed that gene expression levels were up- or downregulated significantly at the stages of young and ripe fruit when compared to plant leaves.

Keywords

Ziziphus jujube RNA-seq gene expression fruit ripening cell wall metabolism 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

11183_2018_7010_MOESM1_ESM.pdf (135 kb)
Supplementary material, approximately 135 KB.

References

  1. 1.
    Liu, M.J. and Cheng, C.Y., A taxonomy study on the genus Ziziphus, Acta Hortic., 1995, vol. 390, pp. 161–165.CrossRefGoogle Scholar
  2. 2.
    Qu, Z. and Wang, Y., Chinese fruit trees record—Chinese jujube, China Forestry Publ. House, 1993.Google Scholar
  3. 3.
    Liu, M.J. and Zhao, Z.H., China Jujube Development Report, 1949–2007, China Forestry Publ. House, 2008.Google Scholar
  4. 4.
    Li, J.W., Ding, S.D., and Ding, X.L., Comparison of antioxidant capacities of extracts from five cultivars of Chinese jujube, Process Biochem., 2005, vol. 40, pp. 3607–3613.CrossRefGoogle Scholar
  5. 5.
    Choi, S.H., Ahn, J.B., Kozukue, N., and Friedman, M., Distribution of free amino acids, flavonoids, total phenolics, and antioxidative activities of jujube (Ziziphus jujuba) fruits and seeds harvested from plants grown in Korea, Agric. Food Chem., 2011, vol. 59, pp. 6594–6604.CrossRefGoogle Scholar
  6. 6.
    Gao, Q.H., Wu, C.S., and Yu, J.G., Textural characteristic, antioxidant activity, sugar, organic acid, and phenolic profiles of 10 promising jujube (Ziziphus jujuba Mill.) selections, J. Food Sci., 2012, vol. 77, pp. 1218–1225.CrossRefGoogle Scholar
  7. 7.
    Giovannoni, J., Molecular biology of fruit maturation and ripening, Annu. Rev. Plant Physiol. Plant Mol. Biol., 2001, vol. 52, pp. 725–729.CrossRefPubMedGoogle Scholar
  8. 8.
    Fabi, J.P., Broetto, S.G., and da Silva, S.L., Analysis of papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softening, PLoS One, 2014, vol. 9: e105685.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Cao, J., Yan, J., and Zhao, Y., Effects of postharvest salicylic acid dipping on Alternaria rot and disease resistance of jujube fruit during storage, J. Sci. Food Agric., 2013, vol. 93, pp. 3252–3258.CrossRefPubMedGoogle Scholar
  10. 10.
    Yan, J., Li, J., and Zhao, H., Effects of oligochitosan on postharvest Alternaria rot, storage quality, and defense responses in Chinese jujube (Zizyphus jujuba Mill. cv. Dongzao) fruit, J. Food Protect., 2011, vol. 74, pp. 783–788.CrossRefGoogle Scholar
  11. 11.
    Verde, I., Abbott, A.G., and Scalabrin, S., The highquality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution, Nat. Genet., 2013, vol. 45, pp. 487–494.CrossRefPubMedGoogle Scholar
  12. 12.
    Sweetman, C., Wong, D.C., and Ford, C.M., Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression, BMC Genomics, 2012, vol. 13:691.CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Grabherr, M.G., Haas, B.J., and Yassour, M., Fulllength transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 2011, vol. 29, pp. 644–652.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Conesa, A., Gotz, S., and García-Gómez, J.M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 2005, vol. 21, pp. 3674–3676.CrossRefPubMedGoogle Scholar
  15. 15.
    Ye, J., Fang, L., and Zheng, H.K., WEGO: a web tool for plotting GO annotations, Nucleic Acids Res., 2006, vol. 34, pp. 293–297.CrossRefGoogle Scholar
  16. 16.
    Audic, S. and Claverie, J.M., The significance of digital gene expression profiles, Genome Res., 1997, vol. 7, pp. 986–995.CrossRefPubMedGoogle Scholar
  17. 17.
    Livak, K.J. and Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2(–Delta Delta C(T)) method, Methods, 2001, vol. 25, pp. 402–408.CrossRefPubMedGoogle Scholar
  18. 18.
    Wu, L.P., Tang, Y., and Li, Y.Y., Estimation of genome size of Ziziphus jujuba and Z. acdiojujuba, J. Beijing For. Univ., 2013, vol. 35, pp. 77–83.Google Scholar
  19. 19.
    Liu, M.J., Zhao, J., and Cai, Q.L., The complex jujube genome provides insights into fruit tree biology, Nat. Commun., 2014, vol. 5, pp. 5312–5315.CrossRefGoogle Scholar
  20. 20.
    Huang, J., Zhang, C.M., Zhao, X., Fei, Z.J., Wan, K.K., Zhang, Z., Pang, X.M., Yin, X., Bai, Y., Sun, X.Q., Gao, L.Z., Li, R.Q., Zhang, J.B., and Li, X.G., The jujube genome provides insights into genome evolution and the domestication of sweetness/Acidity taste in fruit trees, PLoS Genet., 2016, vol. 12: e1006433.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Klee, H.J. and Giovannoni, J.J., Genetics and control of tomato fruit ripening and quality attributes, Annu. Rev. Genet., 2011, vol. 45, pp. 41–59.CrossRefPubMedGoogle Scholar
  22. 22.
    Fray, R.G. and Grierson, D., Molecular genetics of tomato fruit ripening, Trends Genet., 1993, vol. 9, pp. 438–443.CrossRefPubMedGoogle Scholar
  23. 23.
    Brownleader, M.D., Jackson, P., and Mobasheri, A., Molecular aspects of cell wall modifications during fruit ripening, Crit. Rev. Food Sci. Nutr., 1999, vol. 39, pp. 149–164.CrossRefPubMedGoogle Scholar
  24. 24.
    Powell, A.L., Kalamaki, M.S., and Kurien, P.A., Simultaneous transgenic suppression of LePG and LeExp1 influences fruit texture and juice viscosity in a fresh market tomato variety, J. Agric. Food Chem., 2003, vol. 51, pp. 7450–7455.CrossRefPubMedGoogle Scholar
  25. 25.
    Wang, B.M., Ding, G.X., and Wang, X.Y., Changes of histological structure and water potential of Huping jujube fruit cracking, Sci. Agric. Sinica, 2013, vol. 46, pp. 4558–4568.Google Scholar
  26. 26.
    Lu, P.L. and Lin, C.H., Physiology of fruit cracking in wax apple (Syzygium samarangense), Bot. Orient.—J. Plant Sci., 2011, vol. 8, pp. 70–76.Google Scholar
  27. 27.
    Brummell, D.A. and Harpster, M.H., Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants, Plant Mol. Biol., 2001, vol. 47, pp. 311–318.CrossRefPubMedGoogle Scholar
  28. 28.
    Balbontin, C., Ayala, H., and Rubilar, J., Transcriptional analysis of cell wall and cuticle related genes during fruit development of two sweet cherry cultivars with contrasting levels of cracking tolerance, Chil. J. Agr. Res., 2014, vol. 74, pp. 162–169.CrossRefGoogle Scholar
  29. 29.
    Knoche, M., Peschel, S., and Hinz, M., Studies on water transport through the sweet cherry fruit surface. II. Conductance of the cuticle in relation to fruit development, Planta, 2001, vol. 213, pp. 927–936.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  1. 1.College of Agriculture, Institute of Agricultural BiotechnologyShanxi Agricultural UniversityTaigu ShanxiChina
  2. 2.Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess PlateauMinistry of AgricultureTaiyuan ShanxiChina

Personalised recommendations