Comparative Transcriptomic Analysis Identifies Key Cellulose Synthase Genes (CESA) and Cellulose Synthase-like Genes (CSL) in Fast Growth Period of Flax Stem (Linum Usitatissimum L.)

References

• Amor, Y., Haigler, C, H., Johnson, S., WainscottM., and Delmer, D.P. 1995. A membrane-associated form of sucrose synthase and its potential role in synthesis of cellulose and callose in plants. Proceedings of the National Academy of Sciences of the United States of America 92: 9353–9357. doi:10.1073/pnas.92.20.9353.
   PubMed Web of Science ®Google Scholar
• Barvkar, V.T., Pardeshi, V.C., Kale, S.M., Kadoo, N.Y., and Gupta, V.S. 2012. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. BMC Genomics 3(1):175. doi:10.1186/1471-2164-13-175.
   Google Scholar
• Chantreau, M., Chabbert, B., Billiard, S., Hawkins, S. and Neutelings, G. 2015. Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virus-induced gene silencing. Plant Biotechnology Journal 13(9):1312–1324. doi:10.1111/pbi.12350.
   PubMed Web of Science ®Google Scholar
• Dilokpimol, A., Poulsen, C. P., Vereb, G., Kaneko, S., Schulz, A., and Geshi, N. 2014. Galactosyltransferases from Arabidopsis thaliana in the biosynthesis of type II arabinogalactan: molecular interaction enhances enzyme activity. BMC Plant Biology 14:90. doi:10.1186/1471-2229-14-90.
   PubMed Web of Science ®Google Scholar
• Doblin, M.S., Kurek, I., Jacob-Wilk, D., and Delmer, D.P. 2002. Cellulose biosynthesis in plants: from genes to rosettes. Plant and Cell Physiology 43(12):1407–1420. doi:10.1093/pcp/pcf164.
   PubMed Web of Science ®Google Scholar
• Endler, A., and Persson, S. 2011. Cellulose Synthases and Synthesis in Arabidopsis. Molecular Plant 4,199–211. doi:10.1093/mp/ssq079.
   PubMed Web of Science ®Google Scholar
• Galinousky, D., and Padvitski, T. 2017. Analysis of public RNA-seq data in studies of flax fiber biogenesis. The EuroBiotech Journal 1(2):177–179. doi:10.24190/ISSN.2564-615X/2017/02.10
   Google Scholar
• Galinousky, D., Padvitski, T., Bayer, G., Pirko, Y., Pydiura, N., Anisimova, N., Nikitinskaya, T., Khotyleva, L., Yemets, A., Kilchevsky, A., et al. 2019. Expression analysis of cellulose synthase and main cytoskeletal protein genes in flax (Linum usitatissimum L.). Cell Biology Interenational 43(9):1065–1071. doi:10.1002/cbin.10837
   PubMed Web of Science ®Google Scholar
• Galinousky, D., Padvitski, T., Mokshina, N., Gorshkov, O., Khotyleva, L., Gorshkova, T., and Kilchevsky, A. 2020. Expression of cellulose synthase-like genes in two phenotypically distinct flax (Linum usitatissimum L.) subspecies. Genetic Resource and Crop Evolution 67:1821–1837. doi:10.1007/s10722-020-00943-2.
   Web of Science ®Google Scholar
• Gorshkova, T. A., Sal’Nikov, V. V., Chemikosova, S. B., Ageeva, M. V., Pavlencheva, N. V., and Van Dam, J. E. G. 2003. The snap point: a transition point in Linum usitatissimum bast fiber development. Industrial crops and products 18(3):213–221. doi:10.1016/S0926-6690(03)00043-8.
   Web of Science ®Google Scholar
• Gorshkova, T., Chernova, T., Mokshina, N., Gorshkov, V., Kozlova, L., and Gorshkov, O. 2018. Transcriptome analysis of intrusively growing flax fibers isolated by laser microdissection. Scientific Reports 8:14570. doi:10.1038/s41598-018-32869-2.
   PubMed Web of Science ®Google Scholar
• Gorshkov, O., Mokshina, N., Gorshkov, V., Chemikosova, S., Gogolev, Y., and Gorshkova, T., 2017. Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization. Plant Molecular Biology 93(4–5):431–449. doi:10.1007/s11103-016-0571-7.
   PubMed Web of Science ®Google Scholar
• Guo, Y., Qiu, C., Long, S., Chen, P., Hao, D., Preisner, M., Wang, H., and Wang, Y. 2017. Digital gene expression profiling of flax (Linum usitatissimum L.) stem peel identifies genes enriched in fiber-bearing phloem tissue. Gene 626:32–40, 32–40. doi: 10.1016/j.gene.2017.05.002.
   PubMedGoogle Scholar
• Handakumbura, P. P., Brow, K., Whitney, I. P., Zhao, K. M., Sanguinet, K. A., Lee, S. J., Olins, J., Romero-Gamboa, S. P., Harrington, M. J., Bascom, C. J., MacKinnon K.J.M. 2018. SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachy on and is not found in the Brassicaceae. The Plant Journal 96: 532–545. doi: 10.1111/tpj.14047.
   PubMed Web of Science ®Google Scholar
• Hobson, N., and Deyholos, M. K. 2013. Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. BMC Genomics 14(1):344. doi:10.1186/1471-2164-14-344.
   PubMedGoogle Scholar
• Hotte, N.S.C., and Deyholos, M.K. 2008. A flax proteome: identification of proteins enriched in bast fibres. BMC Plant Biology 8(1):52. doi:10.1186/1471-2229-8-52.
   PubMedGoogle Scholar
• Huis, R., Hawkins, S., and Neutelings, G. 2010. Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC Plant Biology 10(1):71. doi:10.1186/1471-2229-10-71.
   PubMedGoogle Scholar
• Liu, L., Shang-Guan, K., Zhang, B., Liu, X., Yan, M., Zhang, L., Shi, Y., Zhang, M., Qian, Q., Li, J., and Zhou, Y. 2013. Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils. PLoS Genetics 9(8):e1003704. doi:10.1371/journal.pgen.1003704.
   PubMed Web of Science ®Google Scholar
• Liwanag, A. J. M., Ebert, B., Verhertbruggen, Y., Rennie, E. A., Rautengarten, C., Oikawa, A., Andersen, M. C. F., Clausen, M. H., and Scheller, H. V. 2012. Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a β-1,4-galactan β-1,4-galactosyltransferase. Plant Cell 24(12):5024–5036. doi:10.1105/tpc.112.106625
   PubMed Web of Science ®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(4): 402–8.
   PubMed Web of Science ®Google Scholar
• Mokshina, N., Gorshkova, T., and Deyholos, M. K. 2014. Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers. PLoS One 9(6):e979499. doi:10.3390/fib6020020.
   Web of Science ®Google Scholar
• Mokshina, N., Gorshkov, O., Ibragimova, N., Chernova, T., and Gorshkova, T. 2017. Cellulosic fibres of flax recruit both primary and secondary cell wall cellulose synthases during deposition of thick tertiary cell walls and in the course of graviresponse. Functional plant biology 44(8):820–831. doi:10.1071/ FP17105
   PubMed Web of Science ®Google Scholar
• Pinzón-Latorre, D., and Deyholos, M.K. 2013. Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum). BMC Genomics 14(1):742. doi:10.1186/1471-2164-14-742.
   PubMedGoogle Scholar
• Pydiura, N., Pirko, Y., Galinousky, D., Postovoitova, A., Yemets, A., Kilchevsky, A., and Blume, Y. 2018. Genome-wide identification, phylogenetic classification, and exon-intron structure characterisation of the tubulin and actin genes in flax (Linum usitatissimum). Cell Biology Interenatinal 43(5). doi:10.1002/cbin.11001.
   Web of Science ®Google Scholar
• Robinson, M.D., McCarthy, D.J., and Smyth, G.K. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. doi: 10.1093/bioinformatics/btp616.
   PubMed Web of Science ®Google Scholar
• Roach, M. J., and Deyholos, M. K. 2008 Microarray analysis of developing flax hypocotyls identifies novel transcripts correlated with specific stages of phloem fibre differentiation. Annals of Botany 102(3):317–330. doi: 10.1093/aob/mcn110.
   PubMed Web of Science ®Google Scholar
• Seifert, G. J., and Roberts, K. 2007. The biology of arabinogalactan proteins. In Annual Review of Plant Biology 58.:137–161. doi:10.1146/annurev.arplant.58.032806.103801.
   PubMed Web of Science ®Google Scholar
• Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D., McDill, J., Yang, L., Hawkins, S., Neutelings, G., Datla, R., et al. 2012. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant Journal 72(3):461–473. doi:10.1111/j.1365-313X.2012.05093.x.
   PubMed Web of Science ®Google Scholar
• Wang, S., Yin, Y.B., Ma, Q., Tang, X.J., Hao, D.Y., and Xu, Y. 2012. Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC Plant Biology 12:138. doi:10.1186/1471-2229-12-138
   PubMed Web of Science ®Google Scholar
• Yin, Y., Johns, M.A., Cao, H., and Rupani, M. 2014. A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. BMC Genomics 15:260. doi:10.1186/1471-2164-15-260.
   PubMed Web of Science ®Google Scholar