昆虫密码子使用偏好性研究进展

doi:10.16288/j.yczz.25-214

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Hereditas(Beijing) ›› 2026, Vol. 48 ›› Issue (2): 158-176.doi: 10.16288/j.yczz.25-214

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Research progress on insect codon usage bias

Shitian He(), Xinyi Zhu, Sihuan Li, Shaomin Tao, Cheng Pan, Chuanlin Yin()

College of Life Sciences, China Jiliang University, Hangzhou 310018, China

Received:2025-08-05 Revised:2025-09-15 Online:2025-10-29 Published:2025-10-29
Contact: Chuanlin Yin E-mail:hestian2023@163.com;chuanlinyin@cjlu.edu.cn
Supported by:
National Natural Science Foundation of China(32202315)

Abstract

Abstract:

Codon usage bias (CUB) refers to the non-random usage of synonymous codons during protein translation. It holds significant value for understanding species evolution, environmental adaptation, gene expression regulation, and population genetic diversity. In this review, we summarize the biological significance of codon usage bias, outline commonly used statistical approaches for its analysis, and provide a comprehensive overview of recent advances in codon usage research within the field of entomology. This work aims to offer new perspective and methodologies insights to support further in-depth studies of codon usage patterns in insects.

Key words: codon usage bias, insect genome evolution, synonymous codons, effective codon number, codon optimization

Shitian He, Xinyi Zhu, Sihuan Li, Shaomin Tao, Cheng Pan, Chuanlin Yin. Research progress on insect codon usage bias[J]. Hereditas(Beijing), 2026, 48(2): 158-176.

Figures/Tables 3

Table 1

Fig. 1

Table 2

Statistics of literature related to insect codon usage bias"

序号	研究对象		基因来源	统计指标	统计分析/研究方法	参考文献
1	鞘翅目金龟子科甲虫		线粒体基因组PCGs	碱基组成、RSCU、ENC、核苷酸偏度、tRNA结构	ENC-plot、pr2-plot、中性图、系统发育分析	[87]
2	双翅目摇蚊科29种昆虫		线粒体基因组CDS	GC3s、ENC、RSCU、核苷酸偏度、ENC-ratio	ENC-plot、聚类热图、Shapiro-Wilk正态性检验、Levene’s方差齐性检验、配对t检验	[117]
3	415种脊索动物与191种节肢动物		线粒体与核基因组CDS	RSCU、突变偏好参数、适应度系数、香农熵、Moran’s I系数	进化模型拟合、模型比较检验、系统发育信号分析、敏感性分析	[118]
4	半翅目睡莲缢管蚜		线粒体基因组	tRNA基因定位与二级结构、RSCU、核苷酸组成、核苷酸偏度、密码子适应指数、Ka/Ks、核苷酸多样性π值	ENC-plot、pr2-plot、中性图、分子进化速率分析、单因素ANOVA、重复序列分析、系统发育分析	[86]
5	双翅目鼻颜蚜蝇属5种昆虫		线粒体基因组	碱基组成、RSCU、ENC	中性图、pr2-plot、ENC-plot、系统发育分析	[119]
6	膜翅目阿里山潜蝇茧蜂		线粒体基因组PCGs	碱基组成、RSCU、ENC、最优密码子	中性图、ENC-plot、相关性分析	[120]
7	鳞翅目7种蝴蝶与1种蛾类		核基因组CDS	GC、dN、dS、ω、GC-conservative、S→W与W→S替换率、RSCU、ENC、tRNA拷贝数、RAIT	分子进化速率分析、GO富集、Kruskal-Wallis检验、多元回归、相关性分析、ENC-plot	[91]
8	半翅目日本小叶蝉属5种昆虫		线粒体基因组PCGs	碱基组成、核苷酸偏度、RSCU	pr2-plot、中性图、对应分析、系统发育分析	[84]
9	鞘翅目灭字脊虎天牛		线粒体基因组CDS	碱基组成、RSCU、最优密码子	相关性分析、中性图、ENC-plot、pr2-plot	[121]
10	双翅目姆加饰腹寄蝇		线粒体基因组CDS	核苷酸偏度、RSCU、dN/dS	选择压力分析、系统发育分析、中性图、ENC-plot、回归分析、主成分分析	[112]
11	双翅目29种果蝇		核基因组CDS	GC含量、ENC、RSCU、sENC-X、tRNA基因数、SDU含量	回归分析、层次聚类、对应分析、非参数Mann-Whitney U检验、Pagel’s λ、ENC-plot	[92]
12	半翅目菜蝽		线粒体基因组CDS	碱基组成、RSCU	相关性分析、ENC-plot、中性图	[122]
13	鳞翅目菜粉蝶中肠表达基因		核基因组CDS	GC含量、ENC、RSCU、最优密码子	异源基因表达分析、基因组定位与结构域分析	[123]
14	蜻蜓目7种蜻蜓与2种豆娘		线粒体基因组PCGs	碱基组成、ENC、RSCU、Ks/Ks	层次聚类热图、t检验、中性图、ENC-plot、分子进化分析	[111]
15	双翅目黑腹果蝇		核基因组CDS	RSCU、GC3、基因表达量(FPKM)、蛋白质长度	对应分析、内部对应分析、置换多元方差分析(PERMANOVA)、置换多元协方差分析(PERMANCOVA)	[102]
16	半翅目30种昆虫		线粒体COI基因	GC含量、ENC、RSCU	聚类分析	[114]
17	12种双翅目与7种膜翅目昆虫		核基因组CDS	RSCU、GC含量、CAI、ENC、SCUO、RSCPU	层次聚类、相关性分析、回归分析、密码子对偏好分析、卡方检验、DTK检验、GO富集、密码子上下文分析	[95]
18	鳞翅目家蚕		核基因组CDS	碱基组成、ENC、ENC-ratio、最优密码子	对应分析、相关性分析、ENC-plot、中性图	[85]
19	半翅目烟粉虱与叶蝉	核基因组CDS		碱基组成、RSCU、ENC、CAI	相关性分析	[89]
20	鳞翅目家蚕与亚洲玉米螟	核基因组CDS		碱基组成、ENC、RSCU	相关性分析	[90]
21	鳞翅目家蚕	线粒体与核基因组CDS		碱基组成、ENC、RSCU	主成分分析、对应分析、回归分析、因子分析、中性图、ENC-plot、聚类分析	[124]
22	双翅目3种蚊子	核基因组CDS		SCUO、ENC、CAI、内含子长度、GC含量	典型相关分析、卡方检验、层次聚类、相关性分析、多因素分析、系统发育分析	[94]
23	昆虫纲3目6种水生昆虫	线粒体基因组PCGs		碱基组成、RSCU、ENC、SCU、高频密码子	相关性分析、ENC-plot、对应分析	[88]
24	双翅目埃及伊蚊和冈比亚蚊	核基因组tRNA与CDS		tRNA基因拷贝数、基因簇结构、RAIT、CBI、RSCU	tRNA基因鉴定与验证、基因组定位、相关性分析、功能富集分析、系统发育分析	[103]
25	膜翅目寄生蜂及其他节肢动物	核基因组tRNA		tRNA基因拷贝数、基因簇结构、RSCU、RAIT、内含子数量、核苷酸多样性	tRNA基因鉴定与注释、基因组定位、相关性分析、系统发育分析	[101]
26	昆虫纲6目49种昆虫	线粒体基因组PCGs、CDS		碱基组成、RSCU、最优密码子、反密码子	密码子使用变异性分析	[125]
27	双翅目黑腹果蝇	核基因组CDS		碱基组成、ENC、Fop、差异表达基因鉴定	ANOVA模型、密码子使用偏好性差异检验、核糖体蛋白表达谱验证	[100]
28	半翅目豌豆蚜	EST组装编码序列		碱基组成、ENC、RSCU、侧翼序列及内含子组成	编码基因组重建与注释、对应分析、ANOVA、ENC-plot、相关性分析	[126]
29	昆虫纲12个目88种昆虫	线粒体COI基因		Total Bias、ENC、GC含量、MCB、ENC′、dS	相关性分析、零模型/单偏好模型/双偏好模型拟合	[113]
30	双翅目果蝇属物种	核基因组CDS		ENC、RSCU、GC3、tRNA基因拷贝数	中性图、系统发育比较分析、相关性分析	[31]
31	鳞翅目5种昆虫	血淋巴蛋白CDS		碱基组成、RSCU、CAI、GC3、内含子GC含量	卡方检验、相关性分析	[99]
32	双翅目冈比亚蚊	核基因组染色体基因和反转录转座子		RSCU、GC3s、ENC、碱基组成	比较基因组分析	[93]

Table 2

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软件/网站/数据库名称	功能	链接	参考文献
CAL calculator	计算E-CAI、RSCU和nCAI等指标、核苷酸组成、密码子使用模式、密码子优化	http://genomes.urv.es/CAIcal/	[67]
OPTIMIZER	优化DNA或蛋白质序列，预测和提升异源基因在宿主中的表达水平	http://genomes.urv.es/OPTIMIZER/	[68]
Kazusa	密码子使用频率、基因序列编译为密码子使用表	https://www.kazusa.or.jp/codon/	[69]
CoCoPUTs	密码子使用表、二核苷酸含量、密码子频率热图、GC含量、ENC和ENCP等指标分析图表	https://ngdc.cncb.ac.cn/databasecommons/database/ id/6462	[70]
EMBOSS	Cusp：核酸序列创建密码子表 Cal：计算密码子适应指数 Chips：密码子使用统计 Syco：绘制同义密码子统计图 Comseq：单个碱基或二、三联体组成频率 Geecee：GC含量	https://www.bioinformatics.nl/emboss-explorer/	[71]
CodonW	密码子相关指标、密码子优化、表达水平预测	http://codonw.sourceforge.net/	[72]
SeqinR	组内对应分析、序列处理及分析	http://pbil.univ-lyon1.fr/datasets/charif04/	[73]
INCA	计算密码子与氨基酸频率、RSCU、ENC和CAI等常见指标，自组织映射(SOM)进行数据可视化分析等	http://bioinfo.hr/research/inca/	[74]
JCAT	基因合成优化及密码子设计	http://www.jcat.de/	[75]
COUSIN	密码子使用相似度索引	http://cousin.ird.fr	[76]
ACUA	核苷酸分析、密码子统计、交互式分析	https://www.bioinsilico.com/automated-codon-usage- analysis-software-acua	[77]
CodonO	计算并优化SCUO指数	https://sysbio.missouri.edu/software/CodonO/fallback	[78]

Research progress on insect codon usage bias

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