Zhao Ruoxuan, Gu Congwei, Zou Xiaoxia, Zhao Mingde, Xiao Wudian, He Manli, He Lvqin, Yang Qian, Geng Yi, Yu Zehui
Laboratory Animal Center, Southwest Medical University, Luzhou, Sichuan, PR China.
Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
Comput Struct Biotechnol J. 2022 Jun 27;20:3493-3502. doi: 10.1016/j.csbj.2022.06.049. eCollection 2022.
Members of the family (iridovirids) are globally distributed and trigger adverse economic and ecological impacts on aquaculture and wildlife. Iridovirids taxonomy has previously been studied based on a limited number of genomes, but this is not suitable for the current and future virological studies as more iridovirids are emerging. In our study, 57 representative iridovirids genomes were selected from a total of 179 whole genomes available on NCBI. Then 18 core genes were screened out for members of the family . Average amino acid sequence identity (AAI) analysis indicated that a cut-off value of 70% is more suitable for the current iridovirids genome database than ICTV-defined 50% threshold to better clarify viral boundaries. In addition, more subgroups were divided at genus level with the AAI threshold of 70%. This observation was further confirmed by genomic synteny analysis, codon usage preference analysis, genome GC content and length analysis, and phylogenic analysis. According to the pairwise comparison analysis of core genes, 9 hallmark genes were screened out to conduct preliminary identification and investigation at the genus level of iridovirids in a more convenient and economical manner.
虹彩病毒科（虹彩病毒）成员分布于全球，对水产养殖和野生动物造成不利的经济和生态影响。虹彩病毒分类学此前是基于有限数量的基因组进行研究的，但随着更多虹彩病毒的出现，这并不适用于当前及未来的病毒学研究。在我们的研究中，从NCBI上可获取的179个全基因组中选择了57个具有代表性的虹彩病毒基因组。然后筛选出18个虹彩病毒科成员的核心基因。平均氨基酸序列同一性（AAI）分析表明，与国际病毒分类委员会（ICTV）定义的50%阈值相比，70%的截止值更适合当前的虹彩病毒基因组数据库，以更好地厘清病毒界限。此外，在属水平上以70%的AAI阈值划分出了更多亚组。基因组共线性分析、密码子使用偏好分析、基因组GC含量和长度分析以及系统发育分析进一步证实了这一观察结果。根据核心基因的成对比较分析，筛选出9个标志性基因，以便以更便捷、经济的方式在虹彩病毒属水平上进行初步鉴定和研究。
