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Archive > Volume 15 Issue 2 > 2023,15(2):284-290. DOI:https://doi.org/10.1016/j.chmed.2022.08.007 Prev Next

柴胡葉綠體基因組序列密碼子偏性分析

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Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome

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    摘要:
    目的：為了有效鑒別柴胡及其偽品及確認柴胡葉綠體基因組序列密碼子使用特點及其影響因素，對柴胡葉綠體進行了測序、組裝并分析了其78個基因的密碼子使用特征。 方法：利用試劑盒提取柴胡葉片的總DNA，利用高通量測序技術對柴胡葉綠體基因組進行測序，對組裝和注釋后的葉綠體基因組進行結構、基因組成及利用Python 腳本、Codon W軟件對其密碼子偏好性進行分析。 結果：柴胡葉綠體基因組大小為 1155,851 bp，共注釋出 132個基因，包含 80 個 CDS 基因、30 個 tRNA 基因和 4 個 rRNA 基因。大多數(shù)的密碼子以A和 T 結尾，中性繪圖、ENC?plot繪圖、PR2?plot分析及對應分析結果表明密碼子使用模式受堿基組成、突變壓力、選擇壓力因素的影響；通過基因高表達篩選密碼子方法確定了 3 個柴胡葉綠體的最優(yōu)密碼子，大多數(shù)的最優(yōu)密碼子以 U 和 A 結尾。 結論：本研究獲得了柴胡葉綠體基因組并分析柴胡葉綠體基因組的密碼子偏好性受到堿基組成、選擇壓力及突變壓力的影響。該結果可為今后擴展柴胡條形碼的研究及開展葉綠體基因組密碼子優(yōu)化、探索物種進化和增加外源基因表達等研究提供參考依據(jù)和理論基礎。

    Abstract:
    Objective: In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns of chloroplast genome, we determine the complete chloroplast (cp) genome of B. falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B. falcatum chloroplast genome. Methods: The total genomic DNA of fresh leaves from a single individual of B. falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2 lg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform. The cp genome of B. falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters. Python script and Codon W were used to calculate the codon usage bias parameters. Results: The full length of B. falcatum cp genome was 155 851 bp, 132 different genes were annotated in this cp genome containing 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The codon usage models tended to use A/T-ending codons. The neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B. falcatum cp genome. Furthermore, three optimal codons were identified and most of these three optimal codons ended with G/U. Conclusion: The cp genome of B. falcatum has been characterized and the codon usage bias in B. falcatum cp genome is influenced by natural selection, mutation pressure and nucleotide composition. The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes, genetic engineering and molecular evolution in B. falcatum.

    關鍵詞:
    柴胡，葉綠體基因組，密碼子

    Keywords:


    Project Supported:
    This work was supported by the National Natural Science Foundation of China (82204567, 81973430), Natural Science Foundation of Hebei Province (H2020201006), Medical Science Foundation of Hebei University (2021B10), China University Student Innovation and Entrepreneurship Training Program Project (2022333), Advanced Talents Incubation Program of the Hebei University (521000981177, 521000981170), and Resources Development of ‘‘Qin Drug” of Shaanxi University of Chinese Medicine Innovation Team Project (2019-QN01).

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