基于三代测序的大秃马勃的rDNA ITS鉴定及其基因组生物信息学分析

rDNA ITS identification and genomic analysis of Calvatia gigantea, the first sequenced species of Lycoperdaceae

摘要:

[背景] 马勃是著名的传统可食用药用真菌，具有多种药理作用，包括抗菌、抗炎、止咳、抗肿瘤和抑制细胞增殖等。目前关于马勃的研究多集中在活性物质的分离提取及其药理药效上，而对马勃基因组遗传信息知之甚少。[目的] 获得马勃真菌的基因组遗传信息，挖掘潜在具有工业应用价值的功能基因。[方法] 联合使用Illumina二代测序技术和PacBio三代测序技术进行基因组测序，并综合使用多种数据库进行基因组结构分析和基因注释，包括GO注释。基于基因组信息，使用rDNA ITS序列进行马勃真菌物种鉴定，并使用dbCAN和antiSMASH进行碳水化合物活性酶和次级代谢物基因簇的鉴定。[结果] 测序获得大小为46.04 Mb基因组，有11 903个蛋白编码基因，包括6 634个GO注释基因。基于基因组中的rDNA ITS序列信息将该菌鉴定为大秃马勃（Calvatia giganted），分析了麦角甾醇和萜类合成相关基因25个，鉴定出317个碳水化合物酶和18个次级代谢物生物合成基因簇，并发掘出1个潜在的、可分泌的抗丹宁α-淀粉酶。[结论] 获得一株马勃真菌基因组，并发掘出潜在的食品工业应用价值的抗丹宁α-淀粉酶和多个新的次级代谢物合成基因簇。这将为马勃真菌遗传进化、功能基因组学研究，以及其在食品工业应用和次级代谢物的药用价值开发提供重要的遗传信息基础。

关键词:马勃;基因组;三代测序;次级代谢物基因簇

Abstract:

[Background] The puffball mushroom is commonly used traditional medicinal edible fungus, which has multiple pharmacological effects, including antimicrobial, anti-inflammatory, anti-tussive, anti-cancer and suppressing cell growth effects. So far, most of the researches on puffball mushrooms have been focused on extraction and pharmacological effect of their bioactive agents. Nevertheless, little is known about the genomic information of puffball mushrooms. [Objective] To acquire genomic information of puffball mushrooms and mine protein-encoding gene of potential application in industry. [Methods] A combination of Illumina and PacBio sequencing technologies was used for genome sequencing, and analysis of genome structure and gene annotation were performed against multiple database, including GO. The sequenced puffball mushroom was subjected to ITS identification, while CAZymes and secondary metabolite biosynthetic gene clusters were identified using dbCAN and antiSMASH, respectively. [Results] The acquired puffball genome was 46.04 Mb in size, encoding 11 903 proteins including GO-annotated genes. Based on the genomic information, the puffball species was identified as Calvatia gigantea using ITS (Internal Transcribed Spacer). A total of 25 genes related to terpene and ergosterol biosynthetic pathway were analyzed, while 317 CAZymes and 18 secondary metabolite biosynthetic gene clusters were identified. In addition, an alpha-amylase from CAZymes was characterized as a potential secretory, tannin-resistant α-amylase. [Conclusion] This study supplied the first sequenced puffball mushroom, and found a potential tannin-resistant α-amylase and multiple new secondary metabolite biosynthetic gene clusters. This study will supply important basic genetic information for genetic evolution and functional researches of puffball mushrooms, their further application in food industry, and development of secondary metabolites of pharmaceutical value.

Key words:Calvatia;genome;third-generation sequencing;secondary metabolite biosynthetic gene clusters