Abstract: 【Aim】 In this study, single nucleotide polymorphism (SNP) and insertion-deletion (InDel) mutation sites were explored and analyzed using previously obtained PacBio single molecule realtime (SMRT) sequencing data of Ascosphaera apis mycelia, aiming to enrich information about SNP and InDel sites in A. apis and to provide a foundation for the development and application of new molecular markers. 【Methods】 SAMtools was employed to survey the full-length transcripts of the PacBio SMRT sequencing data of A. apis mycelia, followed by detection and analysis of SNP and InDel sites by alignment of the full-length transcripts to the reference genome of A. apis (assembly AAP 1.0) with ANNOVAR software. Genes containing SNP and InDel sites were aligned to GO database and KEGG database using related bioinformatic software to gain corresponding function and pathway annotations. 【Results】 A total of 6 743 SNP sites including 6 091 homozygous sites and 652 heterozygous sites were identified in A. apis mycelium and mainly distributed in exons, and the numbers of SNP sites with transition and transversion were 4 887 and 1 856, respectively. Additionally, the most abundant mutation type of the codon of SNP was synonymous single nucleotide mutation. Moreover, genes containing SNP sites could be annotated to 34 GO terms and 76 KEGG pathways. In total, 597 InDel sites including 349 homozygous sites and 248 heterozygous sites were identified and mainly distributed in genic downstream region, and non-frame shift insertion was the most abundant codon mutation type. Furthermore, genes containing InDel sites could be annotated to 39 GO terms and 87 KEGG pathways. 【Conclusion】 We identified a large quantity of SNP and InDel sites of A. apis, pinpointed their mutation type, distribution in genomic functional element and codon mutation type, and uncovered the potential relationship between SNP and InDel sites and the key biological processes.

Key words:  Ascosphaera apis, third-generation sequencing technology, single molecule real-time sequencing, single nucleotide polymorphism, insertion and deletion