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.
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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.
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.
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.
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.
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.
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.
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.
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.
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
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.
Fry, S.C., Cell Wall Biosynthesis, Handbook of Plant Science, Roberts, K., Ed., Wiley, 2007, pp. 276–283.
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.
Kumar, M. and Turner, S., Plant cellulose synthesis: CESA proteins crossing kingdoms, Phytochemistry, 2015, vol. 112, pp. 91–99.
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.
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
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.
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
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
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.
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.
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.
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.
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
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.
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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.
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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
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DOI: https://doi.org/10.3103/S0095452717010121