Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness
Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness
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DOI：
10.1111/jeu.12944
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发表时间：
2022-09-19
影响因子：
2.2
通讯作者：
Haag, Karen L.
中科院分区：
文献类型：
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作者：
de Albuquerque, Nathalia R. M.;Haag, Karen L.
微孢子虫是一种专性的细胞内寄生虫，自发现以来，由于其独特的形态，其分类和起源一直存在争议。早期微孢子虫的分类学研究主要基于孢子超微结构特征、生活史特征和传播方式。然而，仅仅基于这些特征的分类学和系统发生学可能会产生误导。SSU rRNA是用于分类学分类的传统标记，但SSU rRNA在物种水平上解决微孢子虫之间系统发育关系的能力被认为很弱，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），允许基因组之间快速和易于实施的比较测量，以评估原核生物中的物种边界，具有95%的截断值，用于对相同物种的基因组进行分组。由于完整基因组的日益可用性，基因组相关性的度量已被应用于真核微生物分类，如微孢子虫。然而，ANI值的分布和物种划分的截止值尚未在微孢子虫中得到充分的测试。在这项研究中，我们研究了65个公开的微孢子虫基因组的ANI值的分布，并测试了95%的截止值是否是一个很好的估计外切物种的遗传相关性的基础上。
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.