Skip to main content
Log in

Analysis of cellulose synthase gene expression strategies in higher plants using RNA-sequencing data

  • Published:
Cytology and Genetics Aims and scope Submit manuscript

Abstract

The transcriptomes from different organs and tissues of western poplar, eucalyptus, soybean, and common bean were studied. The expression level of cellulose synthase genes was notably different in different types of tissues and organs in studied plants. For common bean and eucalyptus transcriptome, the domination of certain cellulose synthase genes was typical. These prevailing genes made up more than 50% of the total expression pull of cellulose synthases. On the contrary, cellulose synthase expression pulls of western poplar and soybean were distributed between multiple genes. The different expression strategies of CesA-genes may reflect phylogenetic processes that occurred in genomes studied.

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

Access this article

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

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Wang, Z., Gerstein, M., and Snyder, M., RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 2009, vol. 10, no. 1, pp. 57–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Egan, A.N., Schlueter, J., and Spooner, D.M., Applications of next-generation sequencing in plant biology, Am. J. Bot., 2012, vol. 99, no. 2, pp. 175–185.

    Article  CAS  PubMed  Google Scholar 

  3. Strickler, S.R., Bombarely, A., and Mueller, L.A., Designing a transcirptome next-generation sequencing project for a nonmodel plant species, Am. J. Bot., 2012, vol. 99, no. 2, pp. 257–266.

    Article  CAS  PubMed  Google Scholar 

  4. Giorgi, F.M., Del Fabbro, C., and Licausi, F., Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana, Bioinformatics, 2013, vol. 29, no. 6, pp. 717–724.

    Article  CAS  PubMed  Google Scholar 

  5. Chu, Y. and Corey, D.R., RNA sequencing: platform selection, experimental design, and data interpretation, Nucl. Acid Ther., 2012, vol. 22, no. 4, pp. 271–274.

    CAS  Google Scholar 

  6. Finotello, F. and Di Camillo, B., Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis, Brief. Funct. Genom., 2015, vol. 14, no. 2, pp. 130–142.

    Article  Google Scholar 

  7. Ilut, D.C., Coate, J.E., Luciano, A.K., Owens, T.G., May, G.D., Farmer, A., and Doyle, J.J., A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species, Am. J. Bot., 2012, vol. 99, no. 2, pp. 383–396.

    Article  CAS  PubMed  Google Scholar 

  8. Rourke, J.A., Bolon, Y.T., Bucciarelli, B., and Vance, C.P., Legume genomics: understanding biology through DNA and RNA sequencing, Ann. Bot., 2014, vol. 113, no. 7, pp. 1107–1120.

    Article  Google Scholar 

  9. Wakasa, Y., Oono, Y., Yazawa, S., Ozawa, K., Handa, H., Matsumoto, T., and Takaiwa, F., RNA sequencingmediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions, BMC Plant Biol., 2014, vol. 14. doi 10.1186/1471-2229-14-101

  10. Tsukagoshi, H., Suzuki, T., Nishikawa, K., Agarie, S., Ishiguro, S., and Higashiyama, T., RNA-seq analysis of the response of the halophyte Mesembryanthemum crystallinum (ice plant) to high salinity, PLoS One, 2015, vol. 10, no. 2, p. e0118339.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Fry, S.C., Cell Wall Biosynthesis, Handbook of Plant Science, Roberts, K., Ed., Wiley, 2007, pp. 276–283.

    Google Scholar 

  12. Farrokhi, N., Burton, R.A., Brownfield, L., Hrmova, M., Wilson, S.M., Bacic, A., and Fincher, G.B., Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes, Plant Biotechnol. J., 2006, vol. 4, no. 2, pp. 145–167.

    Article  CAS  PubMed  Google Scholar 

  13. Kumar, M. and Turner, S., Plant cellulose synthesis: CESA proteins crossing kingdoms, Phytochemistry, 2015, vol. 112, pp. 91–99.

    Article  CAS  PubMed  Google Scholar 

  14. Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L., Transcript assembly and abundance estimation from RNA-seq reveals thousands of new transcripts and switching among isoforms, Nat. Biotechnol., 2010, vol. 28, no. 5, pp. 511–515.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Zhang, L., Ming, R., Zhang, J., Tao, A., Fang, P., and Qi, J., De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.), MBC Genom., 2015, vol. 16, p. 1062. doi 10.1186/s12864-015-2256-z

    Google Scholar 

  16. Ouyang, K., Li, J., Zhao, X., Que, Q., Li, P., Huang, H., Deng, X., Singh, S.K., Wu, A.-M., and Chen, X., Transcriptomic analysis of multipurpose timber yielding tree Neolamarckia cadamba during xylogenesis using RNASeq, PLoS One, 2016, vol. 11, no. 7, p. e0159407.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Maleki, S.S., Mohammadi, K., and Ji, K.-Sh., Characterization of cellulose synthesis in plant cells, Sci. World J., 2015. Article ID 8641373. http://dx.doi.org/. doi 10.1155/2016/8641373

    Google Scholar 

  18. Zhang, N. and Deyholos, M.K., RNA Seq analysis of the shoot apex of flax (Linum usitatissimum) to identify phloem fiber specification genes, Front. Plant Sci., 2016, vol. 7, p. 950. doi 10.3389/fpls.2016.00950

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Pydiura, N.A., Bayer, G.Ya., Galinouski, D.V., Yemets, A.I., Pirko, Ya.V., Padvitski, T.A., Anisimova, N.V., Khotyleva, L.V., Kolchevski, A.V., and Blume, Ya.B., Bioinformatic search for cellulose synthase genes in flax (Linum usitatissimum) and their phylogenetic analysis, Cytol. Genet., 2015, vol. 49, no. 5, pp. 279–287.

    Article  Google Scholar 

  20. Galinousky, D.V., Anisimova, N.V., Raiski, A.P., Leontiev, V.N., Titok, V.V., and Khotyleva, L.V., Cellulose synthase genes that control the fiber formation of flax (Linum usitatissimum L.), Russ. J. Genet., 2014, vol. 50, no. 1, pp. 26–34.

    Article  Google Scholar 

  21. Mokshina, N., Gorshkova, T., and Deyholos, M.K., Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers, PLoS One, 2014, vol. 9, no. 2, p. e97949.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Shantreau, M., Chabbert, B., Billiard, S., Hawkins, S., and Neutelings, G., Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virusinduced gene silencing, Plant Biotechnol. J., 2015, vol. 13, no. 9, pp. 1312–1324.

    Article  Google Scholar 

  23. Liu, T., Zhu, S., Tang, Q., Chen, P., Yu, Y., and Tang, Sh., De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud), BMC Genom., 2013, vol. 14, p. 125. doi 10.1186/1471-2164-14-125

    Article  CAS  Google Scholar 

  24. Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, Th., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J., Xu, D., Hellsten, U., May, G.D., Yu, Y., Sakura, T., Umezawa, T., Bhattacharyya, M.K., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, Sh., Goodstein, D., Barry, K., Futrell-Griggs, M., Abernathy, B., Du, J., Tian, Zh., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X.-Ch., Shinozaki, K., Nguyen, H.T., Wing, R.A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R.C., and Jackson, S.A., Genome sequence of the palaeopolyploid soybean, Nature, 2010, vol. 463, no. 7278, pp. 178–183.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to D. V. Galinousky.

Additional information

Original Russian Text © Ts.A. Padvitski, D.V. Galinousky, N.V. Anisimova, G.Ya. Baer, Ya.V. Pirko, A.I. Yemets, L.V. Khotyleva, Ya.B. Blume, A.V. Kilchevsky, 2017, published in Tsitologiya i Genetika, 2017, Vol. 51, No. 1, pp. 12–24.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Padvitski, T.A., Galinousky, D.V., Anisimova, N.V. et al. Analysis of cellulose synthase gene expression strategies in higher plants using RNA-sequencing data. Cytol. Genet. 51, 8–17 (2017). https://doi.org/10.3103/S0095452717010121

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.3103/S0095452717010121

Keywords

Navigation