Tabassum Afsha, Ramesh S V, Zhai Ying, Iftikhar Romana, Olaya Cristian, Pappu Hanu R
Department of Plant Pathology, Washington State University, Pullman, WA, United States.
Indian Council of Agricultural Research-Central Plantation Crops Research Institute, Kasaragod, India.
Front Microbiol. 2021 Sep 20;12:633710. doi: 10.3389/fmicb.2021.633710. eCollection 2021.
Iris yellow spot, caused by Iris yellow spot orthotospovirus (IYSV) (Genus: , Family: ), is an important disease of spp. The complete N gene sequences of 142 IYSV isolates of curated sequence data from GenBank were used to determine the genetic diversity and evolutionary pattern. restriction fragment length polymorphism (RFLP) analysis, codon-based maximum likelihood studies, genetic differentiation and gene flow within the populations of IYSV genotypes were investigated. Bayesian phylogenetic analysis was carried out to estimate the evolutionary rate. RFLP analysis of N gene sequences categorized IYSV isolates into two major genotypes ., IYSV Netherlands (IYSV ; 55.63%), IYSV Brazil (IYSV ; 38.73%) and the rest fell in neither group [IYSV other (IYSV ; 5.63%)]. Phylogenetic tree largely corroborated the results of RFLP analysis and the IYSV genotypes clustered into IYSV and IYSV genotypes. Genetic diversity test revealed IYSV to be more diverse than IYSV and IYSV . IYSV and IYSV genotypes are under purifying selection and population expansion, whereas IYSV showed decreasing population size and hence appear to be under balancing selection. IYSV is least differentiated from IYSV compared to IYSV genotype based on nucleotide diversity. Three putative recombinant events were found in the N gene of IYSV isolates based on RDP analysis, however, RAT substantiated two among them. The marginal likelihood mean substitution rate was 5.08 × 10 subs/site/year and 95% highest posterior density (HPD) substitution rate between 5.11 × 10 and 5.06 × 10. Findings suggest that IYSV continues to evolve using population expansion strategies. The substitution rates identified are similar to other plant RNA viruses.
鸢尾黄斑病由鸢尾黄斑正番茄斑萎病毒（IYSV）（属： ，科： ）引起，是 属植物的一种重要病害。利用从GenBank中筛选出的142个IYSV分离株的完整N基因序列来确定其遗传多样性和进化模式。对IYSV基因型群体进行了限制性片段长度多态性（RFLP）分析、基于密码子的最大似然研究、遗传分化和基因流研究。进行贝叶斯系统发育分析以估计进化速率。对N基因序列的RFLP分析将IYSV分离株分为两个主要基因型。即，荷兰鸢尾黄斑病毒（IYSV ；55.63%）、巴西鸢尾黄斑病毒（IYSV ；38.73%），其余的不属于这两组[其他鸢尾黄斑病毒（IYSV ；5.63%）]。系统发育树在很大程度上证实了RFLP分析的结果，IYSV基因型聚为IYSV 和IYSV 基因型。遗传多样性测试表明IYSV 比IYSV 和IYSV 更多样化。IYSV 和IYSV 基因型处于纯化选择和群体扩张状态，而IYSV 显示群体大小在减小，因此似乎处于平衡选择之下。基于核苷酸多样性，与IYSV 基因型相比，IYSV 与IYSV 的分化最小。基于RDP分析，在IYSV分离株的N基因中发现了三个推定的重组事件，然而，RAT证实其中两个。边际似然平均替代率为5.08×10 替换/位点/年，95%最高后验密度（HPD）替代率在5.11×10 和5.06×10 之间。研究结果表明，IYSV继续采用群体扩张策略进行进化。确定的替代率与其他植物RNA病毒相似。
