Genome-wide analysis of the synonymous codon usage patterns in apple
Genome-wide analysis of the synonymous codon usage patterns in apple
复制标题
苹果同义密码子使用模式的全基因组分析
DOI：
10.1016/s2095-3119(16)61333-3
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发表时间：
2016-01-01
影响因子：
4.8
通讯作者：
Zhang Shi-zhong
中科院分区：
文献类型：
--
作者：
Li Ning;Sun Mei-hong;Zhang Shi-zhong
苹果是温带地区重要的木本植物和主要栽培果树。苹果全基因组测序的完成，为全基因组范围内分析同义密码子使用模式提供了极好的机会。本研究采用多变量生物信息学分析方法，揭示苹果同义密码子使用的特点和影响密码子偏好性的主要因素。利用CodonW和SPSS（Statistical Product and Service Solutions）软件对苹果基因组密码子使用模式进行了中性、对应和相关分析，结果表明苹果基因组密码子使用模式受到突变压力和选择约束的影响。同时，编码序列的长度和蛋白质的疏水性也会影响密码子的使用模式。密码子使用模式的分析和最佳密码子的确定为苹果基因工程、基因预测和分子进化研究奠定了重要的理论基础。
Apple (Malusxdomestica) has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by CodonW and SPSS (Statistical Product and Service Solutions) programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.