紫叶苔(Pleuroziapurpurea)线粒体基因组密码子偏好性分析
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国家自然科学基金(32160315, 31760054);海南大学科研启动项目 (KYQD(ZR)-22105)


Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea
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    摘要:

    为了丰富对紫叶苔属遗传基础的认识,探究了紫叶苔(Pleurozia purpurea)线粒体基因组密码子使用的偏好性及其影响因素。首先,基于完整紫叶苔线粒体基因组筛选蛋白编码序列;然后,利用CodonW、EMBOSS explorer计算各基因的GC含量、有效密码子数(ENC)、密码子适应指数(CAI)和同义密码子相对使用度(RSCU)等指标;最后,采用R软件进行参数间的相关性分析并绘图。结果表明:1) 从紫叶苔线粒体基因组中筛选出31条蛋白编码序列,平均GC含量和密码子第 3 位碱基的 GC 含量分别为38.17%和32.28%,ENC和CAI平均值为50.29、0.17,表明密码子偏好使用以A/U结尾的碱基,且密码子偏好性较弱;2) ENC分别与GCall、GC3以及基因编码氨基酸的长度呈极显著正相关,表明GC含量和基因的长度对密码子的偏好有显著影响;3) 中性绘图、ENC-plot和PR2-plot分析表明,突变压力和自然选择等因素共同塑造了密码子的使用偏好性,其中突变是最主要的影响因素;4) 筛选出23个最优密码子,多数以 A/U 结尾。因此,紫叶苔线粒体基因组密码子偏好性较弱,除了主要受突变压力影响外,还受到自然选择、碱基组成和基因长度等因素的影响,研究结果可为苔藓植物线粒体基因组的进化研究提供参考。

    Abstract:

    In order to enrich the understanding of the genetic basis of the genus Pleurozia purpurea, the codon usage bias (CUB) in the mitochondrial genome of Pleurozia purpurea and its main influencing factors were investigated. Firstly, protein-coding sequences were screened based on the complete mitochondrial genome of Pleurozia purpurea. Then, CodonW and EMBOSS explorer were utilized to calculate various metrics for each gene, including GC content, effective number of codons (ENC), codon adaptation index (CAI), and relative synonymous codon usage (RSCU). Finally, correlation analysis between parameters was analyzed and plotted using R software. The results show that: 1) A total of 31 protein-coding sequences are identified from the mitochondrial genome of Pleurozia purpurea, with an average GC content of 38.17% and a GC content of 32.28% for the third base of codons, respectively. The average values for ENC and CAI are 50.29 and 0.17, indicating a preference for codons ending with A/U bases and a relatively weak CUB; 2) ENC exhibits significantly positive correlations with GCall, GC3, and the length of amino acid encoding genes, indicating significant influences of GC content and gene length on CUB; 3) Analyses including neutrality plot, ENC-plot and PR2-plot indicate that mutation pressure and natural selection jointly shaped the CUB, with mutation being the most important influencing factor; 4) A total of 23 optimal codons are selected, most of which end with A/U. Therefore, the CUB in the mitochondrial genome of Pleurozia purpurea is relatively weak, influenced primarily by mutational pressure, and by factors such as natural selection, base composition, and gene length. The research results can provide reference for evolutionary studies of mitochondrial genomes in bryophytes.

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杜梦雪,张 鑫,高 洁,毕 胜,郝杰威,张莉娜.紫叶苔(Pleuroziapurpurea)线粒体基因组密码子偏好性分析[J].河北科技大学学报,2025,46(1):91-99

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  • 收稿日期:2024-04-27
  • 最后修改日期:2024-08-21
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  • 在线发布日期: 2025-01-17
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