title: Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in Camellia sinensis.
abstract: The stearoyl-acyl carrier protein desaturase (SAD) gene widely exists in all kinds of plants. In this paper, the Camellia sinensis SAD gene (CsSAD) sequence was firstly analyzed by Codon W, CHIPS, and CUSP programs online, and then compared with genomes of the tea plant, other species and SAD genes from 11 plant species. The results show that the CsSAD gene and the selected 73 of C. sinensis genes have similar codon usage bias. The CsSAD gene has a bias toward the synonymous codons with A and T at the third codon position, the same as the 73 of C. sinensis genes. Compared with monocotyledons such as Triticum aestivum and Zea mays, the differences in codon usage frequency between the CsSAD gene and dicotyledons such as Arabidopsis thaliana and Nicotiana tobacum are less. Therefore, A. thaliana and N. tobacum expression systems may be more suitable for the expression of the CsSAD gene. The analysis result of SAD genes from 12 plant species also shows that most of the SAD genes are biased toward the synonymous codons with G and C at the third codon position. We believe that the codon usage bias analysis presented in this study will be essential for providing a theoretical basis for discussing the structure and function of the CsSAD gene.
authors.affiliation: Tea Research Institute, Qingdao Agricultural University, Changcheng Road 700#, Chengyang District, Qingdao, Shandong 266109, China. panlulutea@163.com
authors.forename: Lu-Lu
authors.initials: LL
authors.lastname: Pan
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Jian-Hui
authors.initials: JH
authors.lastname: Hu
authors.forename: Zhao-Tang
authors.initials: ZT
authors.lastname: Ding
authors.forename: Chen
authors.initials: C
authors.lastname: Li
mesh_terms: D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D028241:Camellia sinensis / Q000201:enzymology / Q000235:genetics*; D016000:Cluster Analysis; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D006899:Mixed Function Oxygenases / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D014026:Nicotiana / Q000201:enzymology / Q000235:genetics; D014908:Triticum / Q000201:enzymology / Q000235:genetics; D003313:Zea mays / Q000201:enzymology / Q000235:genetics
chemical_list: D003062:Codon; D010940:Plant Proteins; D006899:Mixed Function Oxygenases; C018747:acyl-(acyl-carrier-protein)desaturase
keywords: Camellia sinensis; Clustering analysis; Codon usage bias; SAD gene