Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome
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摘要:
目的：为了有效鉴别柴胡及其伪品及确认柴胡叶绿体基因组序列密码子使用特点及其影响因素，对柴胡叶绿体进行了测序、组装并分析了其78个基因的密码子使用特征。 方法：利用试剂盒提取柴胡叶片的总DNA，利用高通量测序技术对柴胡叶绿体基因组进行测序，对组装和注释后的叶绿体基因组进行结构、基因组成及利用Python 脚本、Codon W软件对其密码子偏好性进行分析。 结果：柴胡叶绿体基因组大小为 1155,851 bp，共注释出 132个基因，包含 80 个 CDS 基因、30 个 tRNA 基因和 4 个 rRNA 基因。大多数的密码子以A和 T 结尾，中性绘图、ENC?plot绘图、PR2?plot分析及对应分析结果表明密码子使用模式受碱基组成、突变压力、选择压力因素的影响；通过基因高表达筛选密码子方法确定了 3 个柴胡叶绿体的最优密码子，大多数的最优密码子以 U 和 A 结尾。 结论：本研究获得了柴胡叶绿体基因组并分析柴胡叶绿体基因组的密码子偏好性受到碱基组成、选择压力及突变压力的影响。该结果可为今后扩展柴胡条形码的研究及开展叶绿体基因组密码子优化、探索物种进化和增加外源基因表达等研究提供参考依据和理论基础。
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.
关键词:
柴胡，叶绿体基因组，密码子
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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).
Mengqi Gao a, Xiaowei Huo b, Liting Lu a, Mengmeng Liu a,*, Gang Zhang c,*. Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome[J]. Chinese Herbal Medicines (CHM),2023,15(2):284-290
