基于PacBio测序数据的蜜蜂球囊菌SNP与InDel位点发掘及分析

doi:10.16380/j.kcxb.2022.02.007

昆虫学报 ›› 2022, Vol. 65 ›› Issue (2): 187-196.doi: 10.16380/j.kcxb.2022.02.007

基于PacBio测序数据的蜜蜂球囊菌SNP与InDel位点发掘及分析

蔡宗兵^1,#, 张文德^1,#, 隆琦¹, 余岢骏¹, 孙明会¹, 吴鹰¹, 许雅静¹, 刘佳美¹, 郭意龙¹, 徐细建³, 陈大福^1,2,*, 郭睿^1,2,*

(1. 福建农林大学动物科学学院(蜂学学院), 福州 350002; 2. 福建农林大学蜂疗研究所, 福州 350002; 3. 江西省养蜂研究所, 南昌 330000)

出版日期:2022-02-20 发布日期:2022-03-10

Exploration and analysis of SNP and InDel sites in Ascosphaera apis based on PacBio sequencing data

CAI Zong-Bing^1,#, ZHANG Wen-De^1,#, LONG Qi¹, YU Ke-Jun¹, SUN Ming-Hui¹, WU Ying¹, XU Ya-Jing¹, LIU Jia-Mei¹, GUO Yi-Long¹, XU Xi-Jian³, CHEN Da-Fu^1,2,*, GUO Rui^1,2,*

(1. College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; 2. Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; 3. Apicultural Research Institute of Jiangxi Province, Nanchang 330000, China)

Online:2022-02-20 Published:2022-03-10

摘要/Abstract

摘要： 【目的】本研究拟利用已获得的蜜蜂球囊菌Ascosphaera apis菌丝的PacBio单分子实时(single molecule real-time, SMRT)测序数据对蜜蜂球囊菌的单核苷酸多态性(single nucleotide polymorphism, SNP)和插入缺失(insertion-deletion, InDel)突变位点进行发掘和分析，旨在丰富蜜蜂球囊菌的SNP和InDel位点信息，并为新型分子标记的开发和应用提供基础。【方法】采用SAMtools对蜜蜂球囊菌菌丝PacBio SMRT测序数据进行全长转录本识别，再利用ANNOVAR软件将识别的全长转录本与蜜蜂球囊菌参考基因组(assembly AAP 1.0)进行比对以检测和分析SNP位点和InDel位点。通过相关生物信息学软件将上述SNP位点和InDel位点基因分别比对GO和KEGG数据库进行功能和通路注释。【结果】在蜜蜂球囊菌菌丝中共鉴定到6 743个SNP位点，主要分布于外显子，包括6 091个纯合位点和652个杂合位点；其中发生转换和颠换的SNP位点分别有4 887和1 856个；SNP位点密码子突变类型中数量最多的是同义单核苷酸突变；SNP位点基因可注释到34个GO条目和76个KEGG通路。共鉴定到597个InDel位点，包括349个纯合位点和248个杂合位点,这些InDel位点在基因下游区分布的数量最多；InDel位点密码子突变类型中非移码插入最为丰富；InDel位点基因可在39个GO条目和87条KEGG通路。【结论】鉴定到蜜蜂球囊菌的大量SNP和InDel位点，明确了SNP和InDel位点的突变类型、基因组功能元件分布和密码子突变类型，并揭示了SNP和InDel位点与关键生物学过程的潜在关联。

关键词: 蜜蜂球囊菌, 第三代测序技术, 单分子实时测序, 单核苷酸多态性, 插入缺失

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

蔡宗兵, 张文德, 隆琦, 余岢骏, 孙明会, 吴鹰, 许雅静, 刘佳美, 郭意龙, 徐细建, 陈大福, 郭睿. 基于PacBio测序数据的蜜蜂球囊菌SNP与InDel位点发掘及分析[J]. 昆虫学报, 2022, 65(2): 187-196.

CAI Zong-Bing, ZHANG Wen-De, LONG Qi, YU Ke-Jun, SUN Ming-Hui, WU Ying, XU Ya-Jing, LIU Jia-Mei, GUO Yi-Long, XU Xi-Jian, CHEN Da-Fu, GUO Rui. Exploration and analysis of SNP and InDel sites in Ascosphaera apis based on PacBio sequencing data[J]. Acta Entomologica Sinica, 2022, 65(2): 187-196.

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基于PacBio测序数据的蜜蜂球囊菌SNP与InDel位点发掘及分析

Exploration and analysis of SNP and InDel sites in Ascosphaera apis based on PacBio sequencing data

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