de Albuquerque Nathalia R M, Haag Karen L
Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
J Eukaryot Microbiol. 2023 Mar;70(2):e12944. doi: 10.1111/jeu.12944. Epub 2022 Sep 19.
Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.
微孢子虫是与真菌相关的专性细胞内寄生虫，自发现以来，由于其独特的形态，它们的分类和起源一直存在争议。早期对微孢子虫的分类学研究基于超微结构的孢子特征、生命周期特征和传播模式。然而，仅基于这些特征的分类学和系统发育可能会产生误导。小亚基核糖体RNA（SSU rRNA）是分类学分类中使用的传统标记，但在物种水平上，SSU rRNA解析微孢子虫之间系统发育关系的能力被认为较弱，因为它可能没有显示出足够的变异来区分密切相关的物种。总体基因组相关性指数（OGRI），如平均核苷酸同一性（ANI），允许在基因组之间进行快速且易于实施的比较测量，以评估原核生物中的物种界限，同一物种基因组分组的截止值为95%。由于完整基因组的可用性不断增加，基因组相关性指标已应用于真核微生物分类学，如微孢子虫。然而，ANI值的分布和物种界定的截止值在微孢子虫中尚未得到充分测试。在本研究中，我们检查了65个公开可用的微孢子虫基因组的ANI值分布，并测试了95%的截止值是否是基于其遗传相关性来界定物种的良好估计。
