Codon Usage Pattern and its Influencing Factors for Mitochondrial CO Genes Among Different Subfamilies of Cerambycidae.

IF 2.1 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemical Genetics Pub Date : 2024-11-14 DOI:10.1007/s10528-024-10967-3

Yuyang Zhang, Huanxi Yu, Buddhi Dayananda, Tao Yu

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引用次数: 0

Abstract

This study examined nucleotide composition and codon usage of mitochondrial CO (cytochrome oxidase) genes from four subfamilies of Cerambycidae. Nucleotide composition analysis of the CO genes revealed an AT-rich pattern in the four subfamilies of Cerambycidae. Furthermore, by analyzing the correlation between the overall nucleotide composition of CO genes and the nucleotide composition of the 3rd codon, we found that mutation pressure and natural selection were the key factors affected the CUB. The regression of GC12 (The average of GC content of the entire gene first and second codon positions) vs GC3 (GC content of the entire gene third codon positions) scattered to a limited value, and all CO genes slope of the regression line was all less than 0.5, indicated that natural selection might have played a significant role in shaping the codon usage bias. ENC plot analysis further supported the predominant influence of natural selection on CUB, aligning with the findings from neutral plot analyses. These novel insights into the codon evolution of CO genes within Cerambycidae significantly contribute to our understanding of codon evolution.

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角蝇科不同亚科线粒体 CO 基因的密码子使用模式及其影响因素。

本研究考察了 Cerambycidae 四个亚科的线粒体 CO（细胞色素氧化酶）基因的核苷酸组成和密码子使用情况。CO 基因的核苷酸组成分析表明，在 Cerambycidae 的四个亚科中，CO 基因的核苷酸组成呈现出富含 AT 的模式。此外，通过分析CO基因整体核苷酸组成与第3密码子核苷酸组成之间的相关性，我们发现突变压力和自然选择是影响CUB的关键因素。GC12（全基因第一和第二密码子位置的 GC 含量的平均值）与 GC3（全基因第三密码子位置的 GC 含量）的回归散点为有限值，且所有 CO 基因的回归线斜率均小于 0.5，表明自然选择可能在形成密码子使用偏向方面发挥了重要作用。ENC 图谱分析进一步证实了自然选择对 CUB 的主要影响，这与中性图谱分析的结果一致。这些关于角雉科 CO 基因密码子进化的新见解极大地促进了我们对密码子进化的理解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biochemical Genetics 生物-生化与分子生物学

CiteScore

3.90

自引率

0.00%

发文量

133

审稿时长

4.8 months

期刊介绍： Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses. Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication. Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses. Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods. Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.