菌物研究2026，Vol.24Issue(2)：132-142,11.DOI:10.13341/j.jfr.2024.1733
26种真菌UGPase基因的密码子使用偏好性与进化分析
Codon Usage Preference and Evolutionary Analysis of UGPase Genes in 26 Fungal Species
摘要
Abstract
To elucidate the codon usage characteristics and evolutionary relationships of the fungal uridine diphosphate glucose pyrophosphorylase gene(UGPase),this study selected UGPase genes from 14 Basidiomycete and 12 Ascomycete species.Using software tools such as CodonW,SPSS,and MEGA,analyses were conducted on codon usage bias,relative synonymous codon usage(RSCU),and clustering patterns of coding sequences(CDS)across 26 fungal UGPase genes.The results indicated that the GC content of UGPase codons among the 26 fungi ranged from 36.9％to 59.2％,with GC content at the third codon position(GC3s)varying between 31.6％and 87.7％.Notably,in Basidiomycetes,12 species exhibited a preference for codons ending with G or C,while in ascomycetes,except for yeasts,the third codon position also showed a bias toward G/C nucleotides.Correlation analyses revealed a highly significant negative correlation between GC3s and the effective number of codons(ENc),and a highly significant positive correlation between GC3s and overall GC content(P＜0.01).Additionally,ENc was significantly positively correlated with amino acid length(L_aa)(P＜0.05)and highly significantly negatively correlated with the codon adaptation index(CAI).ENc plot analyses suggested that codon usage bias in fungal UGPase genes is influenced by both mutational pressure and natural selection,with selection pressure exerting a greater effect in ascomycetes than in basidiomycetes.Parity rule 2 bias analysis indicated a higher pyrimidine content than purine content at the third codon position.Cluster analysis demonstrated that codon usage bias does not consistently correspond with sequence similarity or species evolutionary relationships.Collectively,these findings suggest that most fungal UGPase genes preferentially use codons ending in G or C and that their codon usage bias is shaped by both natural selection and mutational forces.However,the variation in codon usage bias among species implies that it is unsuitable as a reliable marker for inferring evolutionary relationships between fungal species.关键词
尿苷二磷酸葡萄糖焦磷酸化酶/担子菌/子囊菌/密码子偏好性/物种进化Key words
UDP glucose pyrophosphorylase/Basidiomycetes/Ascomycetes/codon usage prefer-ence/species evolution分类
农业科技引用本文复制引用
段昕莲,严俊杰,甘颖,袁滨,林俊彬,韩星,甘炳成..26种真菌UGPase基因的密码子使用偏好性与进化分析[J].菌物研究,2026,24(2):132-142,11.基金项目
中国农业科学院科技创新工程项目(34-IUA-06),国家现代农业产业技术体系项目(CARS-20),四川省科技计划项目(2021YFYZ0026),四川省育种联合攻关项目(2023YZ001) （34-IUA-06）
