Analysis of Synonymous Codon usage of the Complete Chloroplast Genome in Phleum pratense cv. Minshan

文献类型： 外文期刊

第一作者： Cui, Guangxin

作者： Cui, Guangxin;Wang, Chunmei;Yang, Hongshan;Lu, Yuan;Wang, Xiaoli;Zhu, Xinqiang;Zhang, Qian;Duan, Huirong;Wei, Xiaoxing;Gao, Yaqin

作者机构：

关键词： Synonymous codon usage; Chloroplast genome; Natural selection; Phleum pratense L. cv Minshan

期刊名称：INTERNATIONAL JOURNAL OF AGRICULTURE AND BIOLOGY （ 影响因子：0.822； 五年影响因子：0.906 ）

ISSN： 1560-8530

年卷期： 2020 年 24 卷 2 期

页码：

收录情况： SCI

摘要： Timothy (Phleum pretense L.) is extraordinary roughage for racing horses and dairy cows. Phleum pretense L. cv Minshan is the only cultivar in China, and severe variety degeneration restricts its productivity and promotion. Little information on its genetic characteristics is revealed up to now. To fully display the architectures of Minshan chloroplast genome and lay a theory foundation for future gene modification, synonymous codon usage pattern in Minshan including codon nucleotide base preference, optimal codons and the factors affecting synonymous codon usage was inferred. The tools of Codon W, CUSP of EMBOSS were used to calculate nucleotide compositions and codon usage bias parameters. The average ENC value of 49 genes was 49.44, and all CAI values were less than 0.35, suggesting weak preference of synonymous usage in Minshan. Of 10 identified optimal codons, 6 ended with T and 4 ended with A, implying synonymous codons preferred to use A/T ended codons, and these codons were closer to Axis 1 than others. Most points of the coding genes were under the expected curve of ENC plot analysis and except for InfA, a weak correlation between GC(3) and GC(12) in other 48 genes indicated natural selection was the chief contributor in synonymous codon usage bias in Minshan. The results could lay a theory foundation for codon modification of exogenous genes and molecular assisted breeding in the future. (C) 2020 Friends Science Publishers

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