【目的】 东方蜜蜂微孢子虫Nosema ceranae是一种专性侵染成年蜜蜂中肠上皮细胞的单细胞真菌病原，广泛感染世界各地的蜂群。本研究拟利用已获得的东方蜜蜂微孢子虫纯净孢子的高质量转录组数据进行单核苷酸多态性（Single nucleotide polymorphism，SNP）和插入缺失（Insertion-Deletion，InDel）位点的鉴定和分析，旨在丰富东方蜜蜂微孢子虫的SNP和InDel信息，并为新型分子标记的开发提供基础。【方法】 使用GATK软件识别东方蜜蜂微孢子虫的SNP和InDel位点。采用SnpEff软件预测变异位点发生的基因组区域及变异产生的影响。通过相关生物信息学软件分别将SNP和InDel位点所在基因分别比对GO和KEGG数据库，获得相应的功能和通路注释。【结果】 共鉴定到28 195个SNP位点，其中发生转换和颠换的SNP位点分别有21 403和6 792个；上述SNP位点的突变类型有12种，其中最丰富的突变类型为C/T；分布在CDS区的SNP位点最多，其次是基因间区、上游区、下游区和内含子区；最丰富的密码子突变类型是同义突变；SNP位点所在基因可注释到代谢进程、细胞组分和催化活性等43个GO条目以及代谢途径、核糖体和等次生代谢产物的生物合成等85条KEGG通路。共鉴定到2 831个InDel位点，其中分布在基因间区InDel位点最多，分布在CDS区的InDel位点最少；最丰富的密码子突变类型是移码突变；InDel位点所在基因可注释到细胞进程、细胞和结合等38个GO条目以及代谢途径、次生代谢产物的生物合成及核糖体等73条KEGG通路。【结论】 东方蜜蜂微孢子虫中存在大量的SNP和InDel位点，SNP位点的突变类型主要为转换，与其他物种类似；SNP与InDel位点的基因组功能元件分布规律和突变类型具有明显差异；SNP和InDel位点所在基因与东方蜜蜂微孢子虫适应宿主细胞内环境及病原增殖过程具有潜在关系。

[Objectives]  Nosema ceranae is a widespread, single-cell, fungal pathogen that exclusively infects honeybee midgut epithelial cells worldwide. The objective of this study is to identify and analyze single nucleotide polymorphism (SNP) and insertion and deletion (InDel) loci in N. ceranae using high-quality transcriptome data obtained from clean N. ceranae spores, with the aim of developing novel molecular markers. [Methods]  SNP and InDel loci were detected using GATK software. SnpEff software was used to predict genomic regions with mutation sites and the effects caused by mutation. Genes containing SNP or InDel loci were respectively aligned to the GO and KEGG databases to annotate them to corresponding function and pathways. [Results]  A total of 28 195 SNP loci were identified in N. ceranae, 21 403 of which were conversion loci and 6 792 of which were transversion loci. These SNP loci had 12 types of mutation, the most abundant of which was C/T. SNP loci were mainly distributed in the CDS region, followed by the intergenic region, upstream region, downstream region and the intron. In addition, the most common type of mutation codon in SNP loci was synonymous mutation. Genes containing SNP loci were annotated to 43 GO terms, including metabolic process, cellular process and catalytic activity, and 85 KEGG pathways, such as metabolic pathway, ribosome and biosynthesis of secondary metabolites. 2 831 InDel loci were identified, most of which were distributed in the intergenic region with fewest found in the CDS region. In addition, the most abundant type of codon mutation was the frameshift mutation. Genes containing Indel loci were annotated to 38 GO terms, including cellular process, cell and binding, and 73 KEGG pathways including metabolic pathways, the biosynthesis of secondary metabolites and ribosomes. [Conclusion]  There are high numbers of SNP and InDel loci in N. ceranae and, similar to other species, the most common SNP mutation is conversion. The genomic distribution of the functional elements and mutation types of SNP loci are obviously different from those of InDel loci. Genes containing SNP and InDel loci are potentially involved in the adaptation of N. ceranae to the intracellular environment and the proliferation process of this pathogen.