西南农业学报2025，Vol.38Issue(5)：912-919,8.DOI:10.16213/j.cnki.scjas.2025.5.004
柑橘裂皮类病毒(CEVd)的种群结构及遗传变异分析
Analysis of population structure and genetic variation of citrus exocortis viroid(CEVd)
摘要
Abstract
[Objective]Citrus exocortis viroid(CEVd)is a significant pathogen threatening the sustainable development of the global citrus industry.Understanding the composition and genetic variation of the global CEVd population is crucial for CEVd prevention and control.[Method]Based on 306 CEVd whole genome sequences registered in GenBank database,multiple sequence comparison,base variation analy-sis,cluster analysis and phylogenetic analysis were conducted.[Result]The similarity analysis results indicated that 306 CEVd sequences were composed of 249 variants with similar but not completely identical sequences,and the population structure conformed to the quasispecies model.The three major variants were HQ284019 from Chinese citrus,HF954920 from Cyprus bergamot,and HF954917 from Cyprus pomelo,respectively.Compared to the CEVd reference sequence(NC001464),variation regions and variant bases showed some certain preferences.The frequency of purine(AG+GA)transitions(1000 times)was higher than that of pyrimidine(CT+TC)transitions(479 times),with AG transitions occurring most frequently(609 times).Among transversions,AT transversions occurred most frequently(505 times),while CA transversions occurred least frequently(88 times).The distribution of variant sites was uneven across the genome,with some variants ex-hibiting geographical and host specificity.Analysis of the distribution of variants in the CEVd secondary structure revealed that variations oc-curred more frequently in loop regions than in double-stranded regions,with 3147 and 1769 occurrences,respectively,and two new conserved regions were identified.Based on silhouette coefficient evaluation,it was determined that a clustering number of 4 best reflected the internal structure of the sequence data.Results from Hamming distance calculations showed that Cluster 4 had lower intra-cluster similarity compared to the other three clusters,with significant genetic differences among the sequences within the group.Similarity heatmaps and phylogenetic tree results indicated that the similarity distribution of sequences within Cluster 4 was more dispersed,showing significant divergence in genet-ic relationships,which might exert substantial selective pressure on the evolution of CEVd.[Conclusion]These results revealed that CEVd population might undergo substantial variation during evolution with high sequence variation frequency and diverse population structure,provi-ding a certain reference for CEVd monitoring,prevention and control,and pathogenicity research.关键词
柑橘/CEVd/基因组/种群结构/遗传变异Key words
Citrus/CEVd/Genome/Population structure/Genetic variation分类
农业科技引用本文复制引用
夏凯峰,戚志恩,夏思丹,邢飞..柑橘裂皮类病毒(CEVd)的种群结构及遗传变异分析[J].西南农业学报,2025,38(5):912-919,8.基金项目
中央高校基本科研业务费项目(SWU-KR22029) （SWU-KR22029）
