Comparative analysis of expansin gene codon usage patterns among eight plant species

References

• Chakraborty, P., Das, S., Saha, B., Sarkar, P., Karmakar, A., Saha, A., … Saha, A. (2015). Phylogeny and synonymous codon usage pattern of Papaya ringspot virus coat protein gene in the sub-Himalayan region of north-east India. Canadian Journal of Microbiology, 61, 555–564. doi:10.1139/cjm-2015-0172
   PubMed Web of Science ®Google Scholar
• Che, J., Yamaji, N., Shen, R. F., & Ma, J. F. (2016). An Al-inducible expansin gene, OsEXPA10 is involved in root cell elongation of rice. The Plant Journal, 88, 132–142. doi:10.1111/tpj.13237
   PubMed Web of Science ®Google Scholar
• Chen, Y., Han, Y. Y., Kong, X. Z., Kang, H. H., Ren, Y. Q., & Wang, W. (2017). Ectopic expression of wheat expansin gene TaEXPA2 improved the salt tolerance of transgenic tobacco by regulating Na+/K+ and antioxidant competence. Physiologia Plantarum, 159, 161–177. doi:10.1111/ppl.12492
   PubMed Web of Science ®Google Scholar
• Devi, M., & Lyngdoh, R. H. D. (2017). Favored and less favored codon–anticodon duplexes arising from the GC codon family box encoding for alanine: Some computational perspectives. Journal of Biomolecular Structure & Dynamics, 1–21. doi:10.1080/07391102.2017.1308886
   PubMed Web of Science ®Google Scholar
• Ding, A., Marowa, P., & Kong, Y. (2016). Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum). Molecular Genetics & Genomics, 291, 1891–1907. doi:10.1007/s00438-016-1226-8
   PubMed Web of Science ®Google Scholar
• Duret, L., & Mouchiroud, D. (1999). Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences, 96, 4482–4487. Retrieved from http://pbil.univ-lyon1.fr/members/duret/publications/PDF/1999-DuretMouch-PNAS.pdf10.1073/pnas.96.8.4482
   PubMed Web of Science ®Google Scholar
• Geilfus, C. M., Ober, D., Eichacker, L. A., Mühling, K. H., & Zörb, C. (2015). Down-regulation of ZmEXPB6 (Zea mays β-expansin 6) protein is correlated with salt-mediated growth reduction in the leaves of Z. mays L. Journal of Biological Chemistry, 290, 11235–11245. doi:10.1074/jbc.M114.619718
   PubMed Web of Science ®Google Scholar
• Goulao, L. F., Vieira-Silva, S., & Jackson, P. A. (2011). Association of hemicellulose-and pectin-modifying gene expression with Eucalyptus globulus secondary growth. Plant Physiology and Biochemistry, 49, 873–881. doi:10.1016/j.plaphy.2011.02.020
   PubMed Web of Science ®Google Scholar
• Hutchison, K. W., Singer, P. B., McInnis, S., Diaz-Sala, C., & Greenwood, M. S. (1999). Expansins are conserved in conifers and expressed in hypocotyls in response to exogenous auxin. Plant Physiology, 120, 827–832. doi:10.1104/pp.120.3.827
   PubMed Web of Science ®Google Scholar
• Li, A. X., Han, Y. Y., Wang, X., Chen, Y. H., Zhao, M. R., Zhou, S. M., & Wang, W. (2015). Root-specific expression of wheat expansin gene TaEXPB23 enhances root growth and water stress tolerance in tobacco. Environmental and Experimental Botany, 110, 73–84. doi:10.1016/j.envexpbot.2014.10.002
   Web of Science ®Google Scholar
• Li, X. Y., Li, S. Y., Lang, Z. H., Zhang, J., Zhu, L., & Huang, D. F. (2013). Chloroplast-targeted expression of the codon-optimized truncated cry1Ah gene in transgenic tobacco confers a high level of protection against insects. Plant Cell Reports, 32, 1299–1308. doi:10.1007/s00299-013-1444-z
   PubMed Web of Science ®Google Scholar
• Li, J., Li, H. Y., Zhi, J. K., Shen, C. Z., Yang, X. S., & Xu, J. C. (2017). Codon usage of expansin genes in Populus trichocarpa. Current Bioinformatics, 12, 452–461. doi:10.2174/1574893611666161008195145
   Web of Science ®Google Scholar
• Lin, T., Ni, Z., Shen, M., & Chen, L. (2002). High-frequency codon analysis and its application in codon analysis of tobacco. Journal of Xiamen University, 41, 551–554.
   Google Scholar
• Liu, Q., Feng, Y., & Dong, H. (2004). Comparative studies on synonymous codon usage bias in twenty species. Journal of Northwest Sci-Tech University of Agriculture and Forestry, 32(7), 67–71. Retrieved from http://europepmc.org/abstract/cba/596165
   Google Scholar
• Liu, H. B., Li, H. Y., Zhang, H., Li, J., Xie, B. L., & Xu, J. C. (2016). The expansin gene PttEXPA8, from poplar (Populus tomentosa) confers heat resistance in transgenic tobacco. Plant Cell, Tissue and Organ Culture (PCTOC), 126, 353–359. doi:10.1007/s11240-016-1003-8
   Web of Science ®Google Scholar
• Lü, P. T., Kang, M., Jiang, X. Q., Dai, F. W., Gao, J. P., & Zhang, C. Q. (2013). RhEXPA4, a rose expansin gene, modulates leaf growth and confers drought and salt tolerance to Arabidopsis. Planta, 237, 1547–1559. doi:10.1007/s00425-013-1867-3
   PubMed Web of Science ®Google Scholar
• McQueen-Mason, S., & Cosgrove, D. J. (1994). Disruption of hydrogen bonding between plant cell wall polymers by proteins that induce wall extension. Proceedings of the National Academy of Sciences, 91, 6574–6578. Retrieved from http://www.personal.psu.edu/users/f/s/fsl/ExpCentral/reprints/SMM_CosPNAS94.pdf10.1073/pnas.91.14.6574
   PubMed Web of Science ®Google Scholar
• Murray, E. E., Lotzer, J., & Eberle, M. (1989). Codon usage in plant genes. Nucleic Acids Research, 17(2), 477–498. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/264462110.1093/nar/17.2.477
   PubMed Web of Science ®Google Scholar
• Pan, Q., Wendel, J., & Fluhr, R. (2000). Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. Journal of Molecular Evolution, 50, 203–213. doi:10.1007/s002399910023
   PubMed Web of Science ®Google Scholar
• Park, C. H., Kim, T. W., Son, S. H., Hwang, J. Y., Lee, S. C., Chang, S. C., … Kim, S. K. (2010). Brassinosteroids control AtEXPA5 gene expression in Arabidopsis thaliana. Phytochemistry, 71, 380–387. doi:10.1016/j.phytochem.2009.11.003
   PubMed Web of Science ®Google Scholar
• Peng, Z., Qi, Z., Xu, J. C., & Huang, B. R. (2011). Cloning and Characterization of a Gene, AsEXP1, encoding expansin proteins inducible by heat stress and hormones in creeping bentgrass. Crop Science, 51, 333–341. doi:10.2135/cropsci2010.07.0391
   Web of Science ®Google Scholar
• Perini, M. A., Sin, I. N., Villarreal, N. M., Marina, M., Powell, A. L. T., Martínez, G. A., & Civello, P. M. (2017). Overexpression of the carbohydrate binding module from Solanum lycopersicum expansin 1 (Sl-EXP1) modifies tomato fruit firmness and Botrytis cinerea susceptibility. Plant Physiology and Biochemistry, 113, 122–132. doi:10.1016/j.plaphy.2017.01.029
   PubMed Web of Science ®Google Scholar
• Prabha, R., Singh, D. P., Sinha, S., Ahmad, K., & Rai, A. (2017). Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes. Marine Genomics, 32, 31–39. doi:10.1016/j.margen.2016.10.001
   PubMed Web of Science ®Google Scholar
• Sadhasivam, A., & Vetrivel, U. (2017). Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification. Journal of Biomolecular Structure & Dynamics, 1–25. doi:10.1080/07391102.2017.1343685
   PubMed Web of Science ®Google Scholar
• Sonawane, K. D., Kamble, A. S., & Fandilolu, P. M. (2017). Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNAlys. Journal of Biomolecular Structure & Dynamics, 1–15. doi:10.1080/07391102.2017.1417911
   PubMed Web of Science ®Google Scholar
• Sueoka, N. (2001). Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses. Journal of Molecular Evolution, 53, 469–476. doi:10.1007/s002390010237
   PubMed Web of Science ®Google Scholar
• Suzuki, H., Oshita, E., Fujimori, N., Nakajima, Y., Kawagoe, Y., & Suzuki, S. (2015). Grape expansins, VvEXPA14 and VvEXPA18 promote cell expansion in transgenic Arabidopsis plant. Plant Cell, Tissue and Organ Culture (PCTOC), 120, 1077–1085. doi:10.1007/s11240-014-0662-6
   Web of Science ®Google Scholar
• Takhtajan, A. L. (1954). Proischoždenie pokrytosemennych rastenij. Moskva: Nauka.
   Google Scholar
• van Hemert, F., & Berkhout, B. (2016). Nucleotide composition of the Zika virus RNA genome and its codon usage. Virology Journal, 13, 95–104. doi:10.1186/s12985-016-0551-1
   PubMed Web of Science ®Google Scholar
• Wang, X. T., Li, H. Y., & Xu, J. C. (2014). Bioinformatics analysis of the heavy metal transporting ATPase gene family in poplar genome. Plant Physiology Journal, 50, 891–900.
   Google Scholar
• Xu, J. C., Tian, J., Belanger, F. C., & Huang, B. R. (2007). Identification and characterization of an expansin gene AsEXP1 associated with heat tolerance in C3 Agrostis grass species. Journal of Experimental Botany, 58, 3789–3796. doi:10.1093/jxb/erm229
   PubMed Web of Science ®Google Scholar
• Zhang, L., Jin, L. G., Luo, L., Wang, Y. P., Dong, Z. M., Shu, S. H., & Qiu, L. J. (2011). Analysis of nuclear gene codon bias on soybean genome and transcriptome. Acta Agromica Sinica, 37, 965–974. doi:10.1016/S1875-2780(11)60028-X
   Google Scholar
• Zhao, Y., Yang, P. D., Liu, Z., Cheng, Y., & Yang, Y. (2016). Characterization of codon usage of actin genes for 13 species of plants. Journal of Southern Agriculture, 47(4), 519–523. doi:10.3969/j:issn.2095-1191.2016.04.519
   Google Scholar