Codon Usage Bias of Chalcone Synthase Gene CHS in Kiwifruit
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摘要: 为了解猕猴桃查尔酮合成酶基因（Chalcone Synthase，CHS）的密码子使用特征，采用CodonW、SPSS、MEGA软件和EMBOSS在线程序等分析猕猴桃CHS密码子偏好性，并构建单双子叶植物CHS系统发育树。研究结果表明，猕猴桃CHS有效密码子数（ENc）、总G和C含量（GC）和密码子第3位上G或C含量（GC3s）分别为57.21、0.533和0.607；同义密码子相对使用度（RSCU）大于1.0的密码子数为30，但不存在偏好性极强的密码子；聚类分析结果发现，基于密码子使用偏好性分类可将单双子叶进行准确归类，而CHS序列相似性聚类结果并不理想；密码子使用频率分析表明，猕猴桃CHS与模式生物拟南芥和大肠杆菌基因组间密码子使用偏好性差异相对较小。研究认为，猕猴桃CHS密码子偏好性较弱，但倾向使用G和C，且以G或C结尾的密码子；单双子叶植物CHS间存在严格的密码子使用法则；此外，拟南芥和大肠杆菌可能是猕猴桃CHS遗传转化和异源表达较为理想的受体系统。Abstract: To investage codon usage characteristic of chalcone synthase gene of kiwifruit, CodonW, SPSS, MEGA software and EMBOSS online program were used to analyse codon usgae bias (CUB) of CHS, and phylogenetic tree of CHS between monocotyledon and dicotyledon was constructed in this paper. The results showed that, the effective number of codons (ENc), total GC content (GC) and GC content on the 3rd site (GC3s) was 57.21, 0.533 and 0.607, respectively. The number of condons, the number of relative synonymous codon usage (RSCU) of which was more than 1.0, was 30, but no codons was with strongly CUB. The cluster tree of CHS based on CUB was closer to the real category system than it did by sequence similarity. According to codon usage frequency, the CUB between CHS of kiwifruit and Arabidopsis thaliana, Escherichia coli were more similar. These results indicated that, the CUB level of CHS was low in kiwifruit, but it was bias toward GC rich codons and synonymous codons with G or C at 3rd codon position. And CHS in monocotyledons and dicotyledons had the distinctive CUB rules. In addition, Arabidopsis thaliana and Escherichia coli migth be the best receptors for genetic transformation and heterologous expression of CHS in kiwifruit.
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Key words:
- Kiwifruit /
- chalcone synthase /
- codon usage bias /
- cluster analysis
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图 1 基于密码子使用偏好性(A)和序列相似性(B)CHS聚类分析
Figure 1. Phylogenetic tree analysis of CHS based on CUB (A) and sequence similarity (B)
图 2 猕猴桃CHS与模式基因组密码子使用频率比较
Figure 2. Comparison of CUB between kiwifruit CHS and representative organism genome
表 1 猕猴桃CHS同义密码子相对使用度
Table 1. RSCU of kiwifruit CHS in Actinidia chinensis Planch
氨基酸 密码子 RSCU 丙氨酸Ala GCA 0.75 GCC 1.63 GCG 0.50 GCT 1.13 精氨酸Arg AGA 0 AGG 1.76 CGA 0.35 CGC 1.76 CGG 1.06 CGT 1.06 天冬酰胺Asn AAC 1.78 AAT 0.22 天冬氨酸Asp GAC 1.16 GAT 0.84 半胱氨酸Cys TGC 1 TGT 1 谷氨酰胺Gln CAA 0.91 CAG 1.09 GAA 0.67 GAG 1.33 甘氨酸Gly GGA 0.52 GGC 0.77 GGG 1.42 GGT 1.29 组氨酸His CAC 0.75 CAT 1.25 异亮氨酸Ile ATA 0.32 ATC 1.42 ATT 1.26 亮氨酸Leu CTA 0.57 CTC 1.86 CTG 0.86 CTT 0.86 TTA 0.29 TTG 1.57 赖氨酸Lys AAA 0.67 AAG 1.33 苯丙氨酸Phe TTC 0.77 TTT 1.23 脯氨酸Pro CCA 0.80 脯氨酸Pro CCC 1.40 CCG 0.60 CCT 1.20 丝氨酸Ser AGC 1.64 AGT 1.09 TCA 0.82 TCC 1.09 TCG 0.55 TCT 0.82 苏氨酸Thr ACA 0.17 ACC 1.57 ACG 0.87 ACT 1.39 酪氨酸Tyr TAC 1.33 TAT 0.67 缬氨酸Val GTA 0.13 GTC 1.29 GTG 1.42 GTT 1.16 注：下划线表示偏好性较强的密码子。 
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