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园艺学报 ›› 2012, Vol. 39 ›› Issue (7): 1341-.

• 其它园艺植物 • 上一篇    下一篇

茶树抗寒调控转录因子 ICE1 密码子偏性分析

时 慧, 王 玉, 杨路成, 丁兆堂   

  1. 青岛农业大学茶叶研究所,山东青岛 266109
  • 出版日期:2012-07-25 发布日期:2012-07-25

Analysis of Codon Bias of the Cold Regulated Transcription Factor ICE1 in Tea Plant

 SHI   Hui, WANG   Yu, YANG  Lu-Cheng, DING  Zhao-Tang   

  1. Institute of Tea Science,Qingdao Agricultural University,Qingdao,Shandong 266109,China
  • Online:2012-07-25 Published:2012-07-25

摘要: 运用CHIPS、CUSP 和CodonW 软件程序分析自主克隆的茶树(Camellia sinensis)ICE1(GenBank 登录号JX029153)的密码子的偏性,并与茶树基因组及萝卜等7 种植物的ICE1 密码子偏性进行比较。结果表明,茶树ICE1 偏好于以A/T 结尾的密码子;与茶树基因组密码子偏性相比,发现只有6 种氨基酸密码子偏性完全一致。进一步研究发现ICE1 的碱基组成在单子叶植株大麦与7 种双子叶植物分化后发生了较大的变化。在聚类分析中,基于基因CDS 序列的聚类不能正确反映物种间的进化关系,而基于密码子偏性参数相对密码子使用度(RSCU)的聚类更适合作为系统发育分析的参考。与3 种外源受体密码子使用频率比较发现,与大肠杆菌基因组密码子使用频率差值较大的有25 个,与酵母基因组差值较大的有15 个,与拟南芥基因组差值较大的有10 个,这预示着ICE1 在拟南芥中的表达效率最高,若要在其他外源受体中进行高效表达,尚需对其密码子进行优化。

关键词: 茶树, ICE1, 密码子用法, 密码子偏性, 聚类分析, 抗寒

Abstract: In this study the coding sequence of the ICE1(GenBank Accession No. JX029153)in tea plant(Camellia sinensis)were analyzed with CodonW,CHIPS(Condon heterozygosity in a protein coding sequence)and CUSP(Create a codon usage table)programs,while compared with the genome of tea plant and ICE1 from 7 plant species. The results showed that ICE1 of tea plant was bias toward the synonymous codons with A and T. Compared with the codon usages of tea genome,the consequence indicated that only six kinds of amino acid codon bias was exactly the same. Further studies found that the ICE1 bases composition had greatly changed after monocotyledonous and dicotyledonous plants differentiating. The cluster tree based on the relative synonymous codon usage(RSCU)could not reveal the evolutional relations among the 8 plant species,whereas that based on the relative synonymous codon usage(RSCU)could reveal their evolutional relationship much better. There are 25 codons showing distinct usage differences between ICE1 of tea plant and genome of Escherichia coli,15 between ICE1 of tea plant and genome of yeast,10 between ICE1 of tea plant and genome of Arabidopsis thaliana. Therefore,the Arabidopsis thaliana expression system may be more suitable for the expression of ICE1 of tea plant.

Key words: tea plant, Camellia sinensis, ICE1, codon usage, codon usage bias, cluster analysis, cold resistance

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