Genome-wide comparative analysis of the codon usage patterns in plants
Genome-wide comparative analysis of the codon usage patterns in plants
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植物密码子使用模式的全基因组比较分析
DOI：
10.1007/s13258-016-0417-3
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发表时间：
2016-08-01
期刊：
影响因子：
2.1
通讯作者：
Zhang, Shizhong
中科院分区：
文献类型：
--
作者：
Li, Ning;Li, Yuanyuan;Zhang, Shizhong
密码子使用分析几十年来一直是一个经典的研究领域，对进化、mRNA翻译和新基因发现都很重要。最近，基因组测序使得对植物界的整个基因组进行研究成为可能。分析了该基因编码序列的碱基组成、密码子使用模式、密码子对以及相对同义密码子使用（RSCU）的相关指标，包括Fop、Nc、RSCU、CAI和GC含量。我们发现单细胞藻类的GC含量最高，而双子叶植物最低。此外，植物的基本组成在同一科中是相似的。此外，密码子第二个碱基的GC含量低于第一个和第三个碱基。总之，禾本科、单细胞藻类、蕨类和双子叶植物、苔藓和松科的密码子使用特征相反。此外，密码子使用偏好的程度随着进化而降低。因此，我们假设植物越低，它们必须优化密码子，而高等植物不再需要优化密码子。
Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons.