谷子类甜蛋白基因家族的鉴定与密码子偏性分析
Identification and Codon Bias Analysis of Thaumatin-like Protein Gene Family in Foxtail Millet

类甜蛋白在植物的生长发育和抵御胁迫过程中发挥作用。利用生物信息学方法对谷子类甜蛋白家族基因组成、结构、启动子顺式作用元件、密码子使用偏性等进行分析。结果表明，谷子类甜蛋白家族包含43个成员，分布在9条染色体上，分为3种基因结构类型，其中16个成员仅包含1个外显子，14个包含3个外显子成员的内含子相位均为1-2型。根据系统发育分析归为12个聚类组，聚类组5中的基因主要来自Ⅲ号染色体，聚类组6中的基因主要来自Ⅰ号染色体，其内含子相位多为1-2型，这些基因可能来自同一祖先基因，与进化过程中的染色体重组事件有关。88.4%的基因参与应激反应，多个基因启动子区含有激素和胁迫响应元件，说明该家族基因在植物抵御胁迫过程中发挥作用。多数基因有效密码子数（ENC）较小，密码子的第3位的G+C含量 （GC3s）值分布集中，包含10个最优密码子，均以G或C结尾，表明谷子类甜蛋白家族基因密码子使用偏性强，基因表达潜力高，进化过程中主要受自然选择压力影响。
The thaumatin-like proteins(TLP) play a role in plant growth, development and stress resistance. The composition, structure, cis-acting element and codon usage bias of TLP family of foxtail millet were analyzed by bioinformatics. The results showed that the foxtail millet TLP family consists of 43 members, distributing on nine chromosomes and being divided into three kinds of gene structure types. Sixteen of 43 members contains merely one exon, and introns phase of 14 members possessing three exons belong to 1-2 type. Phylogenetic analysis classifies into twelve clusters , genes of group five and six are mainly from chromosome Ⅲ and Ⅰ, respectively, and most of the intron phase is 1-2 type. These genes may be originated from the same ancestor, and correlated to the evolution events of chromosome recombination. 88.4% genes are involved in stress responses, and multiple gene promoter regions contain hormones and stress responsive elements, indicating that TLP genes play a role in stress resistance.ENC values of most genes are smaller, the distribution of GC3s value is centralized, and 10 optimal codons ended in G or C are found. It is suggested that codon usage in TLP family of foxtail millet is biased, gene expression of potential is high, and is mainly influenced by natural selection pressure during evolution.