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作物学报 ›› 2011, Vol. 37 ›› Issue (06): 965-974.doi: 10.3724/SP.J.1006.2011.00965

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

大豆基因组和转录组的核基因密码子使用偏好性分析

张乐1,金龙国1,罗玲1,王跃平1,董志敏1,孙守红2,邱丽娟1,*   

  1. 1 国家农作物基因资源与遗传改良重大科学工程 / 农业部作物种质资源利用重点开放实验室 / 中国农业科学院作物科学研究所，北京100081; 2 中国科学院遗传与发育研究所，北京100101
  • 收稿日期:2010-12-23 修回日期:2011-03-28 出版日期:2011-06-12 网络出版日期:2011-04-12
  • 通讯作者: 邱丽娟, E-mail: qiu_lijuan@263.net
  • 基金资助:

    本研究由国家高技术研究发展计划(863计划)项目(2006AA10A110)，国家自然科学基金项目(30871621)和国家转基因生物新品种培育科技重大专项重点课题(2009ZX08009-088B)资助。

Analysis of Nuclear Gene Codon Bias on Soybean Genome and Transcriptome

ZHANG Le1,JIN Long-Guo1,LUO Ling1,WANG Yue-Ping1,DONG Zhi-Min1,SUN Shou-Hong2,QIU Li-Juan1,*   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 2 Chinese Academy of Sciences, Beijing 100101, China
  • Received:2010-12-23 Revised:2011-03-28 Published:2011-06-12 Published online:2011-04-12
  • Contact: 邱丽娟, E-mail: qiu_lijuan@263.net

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2696

被引次数

50

摘要： 研究大豆核基因密码子的使用模式，探讨影响其密码子组成和编码特点的因素，为运用基因工程技术提高改良大豆提供理论依据。以大豆基因组的46 430个高置信编码基因和2 071条大豆全长转录本序列为数据来源，应用CodonW软件对大豆全基因组密码子组成、同义密码子使用频率和全长转录组编码区密码子使用各项参数的计算和统计分析发现，基因的表达水平与编码区G+C和GC3s含量均呈极显著正相关，且G+C和GC3s含量越高的基因密码子使用偏好性越高，并确定了UCC和GCC为大豆最优密码子。编码区长度分组分析表明，密码子使用偏好性随编码区长度的增加而降低，编码区较长的基因则趋向于随机使用密码子，且在转录组数据范围内，编码区长度介于400~600 bp的基因表达水平最高。大豆叶片和种子中特异表达基因的密码子使用偏好性和基因表达水平较为接近，但种子特异表达基因的G+C和GC3s含量均显著高于叶片特异表达基因，而其芳香族氨基酸含量则极显著低于叶片特异表达基因。

关键词: 大豆, 基因组, 转录组, 密码子

Abstract: Research of soybean nuclear gene codon composition, usage pattern and influencing factors can provide theoretical basis for applying genetic engineering techonology to improve soybean varieties. A total of 46 430 high confidence coding sequences predicted from soybean genome and 2 071 full-length transcripts were used to analyze the composition and characteristics of soybean nuclear gene codons. CodonW software was applied to calculate the nucleotide composition, relative synonymous codon usage and other parameters of soybean genome and transcriptome. The result indicted that gene expression level was significantly and positively correlated with G+C and GC3s contents, and genes with high G+C and GC3s contents had high codon preference. UCC and GCC were identified as optimal codons in soybean. Analysis of coding sequences with different length showed that codon preference reduced as the coding sequence (CDS) length increased, and longer CDS tend to select codons randomly. CDS length between 400 to 600 bp had the highest expression level among the transcriptome data. The preference and expression level were almost the same between leaf-specific and seed-specific genes. But seed-specific genes had significantly higher G+C and GC3s contents than leaf-specific genes, and the contents of aromatic amino acids encoded by seed-specific genes were highly significantly lower than these by leaf-specific genes.

Key words: Soybean, Genome, Transcriptome, Codon

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