一株稀有海洋真菌Stachybotrys longispora FG216的De Novo测序及基因组学分析

De novo sequencing and genomics analysis of a rare marine fungus Stachybotrys longispora FG216

摘要:

[背景] 长孢葡萄穗霉菌（Stachybotrys longispora）FG216是一株稀有海洋真菌，其次生代谢产物FGFC1具有纤溶活性。进行S.longispora FG216的基因组序列分析，将充实和促进海洋微生物功能基因和次生代谢产物合成生物学的基础研究和应用研究。[目的] 解析S.longispora FG216的基因组序列，分析基因组生物功能和同源相似性关系，分析次生代谢产物纤溶活性化合物FGFC1的相关基因。[方法] 基于Illumina HiSeq高通量测序平台对S.longispora FG216菌株进行De Novo测序，使用SSPACE、Augustus等软件进行组装、编码基因预测、基因功能注释、物种共线性分析以及预测FGFC1次生代谢产物合成基因簇。[结果] S.longisporaFG216的基因组测序总长度为45 622 830 bp，共得到605个Scaffold，GC含量为51.31%，注释预测得到13 329个编码基因和169个非编码RNA。基因组测序数据提交至国家微生物科学数据中心（编号为NMDC60016264），其中13 053、8 422、8 460、7 714和2 847个基因分别能够在NR、KEGG、KOG、GO和CAZy数据库匹配到注释信息。比较基因组学分析发现，Stachybotrys具有保守性，核心基因占基因家族总数目的71.44%，S.longispora FG216与S.chlorohalonata IBT 40285的相似性最高；同时，预测得到101个次生代谢产物合成基因簇，其中18个基因簇与已知的化合物相匹配。通过antiSMASH预测，Cluster 57是编码合成FGFC1母核结构异吲哚啉酮的基因簇，与S.chlorohalonata IBT 40285中的基因簇相似度为40%。[结论] 海洋稀有真菌S.longispora FG216的基因组信息已上传至国家微生物科学数据中心公开使用，为Stachybotrys种属的研究提供了重要的参考意义，同时发现了S.longispora FG216次生代谢产物纤溶活性化合物FGFC1母核部分编码基因是Cluster 57。

Abstract:

[Background] Stachybotrys longispora FG216 is a rare marine fungus, and its secondary metabolite FGFC1 has fibrinolytic activity. The genome sequence analysis of S. longispora FG216 will enrich and promote the basic research and applied research of synthetic biology of marine microbial functional genes and secondary metabolites. [Objective] To detected the genome sequence of S. longispora FG216, analyze the biological function and homologous similarity relation of the genome, and reveal the related secondary metabolite genes of the fibrinolytic active compound FGFC1. [Methods] Based on Illumina HiSeq high-throughput sequencing platform, S. longispora FG216 strain was de novo sequenced. SSPACE, Augustus and other software were used to perform assembly, encoding gene prediction, gene function annotation, species collinear analysis and prediction of FGFC1 secondary metabolite synthesis gene cluster. [Results] The total sequence length of S. longispora FG216 genome was 45 622 830 bp, and a total of 605 scaffolds were obtained, with a GC content of 51.31%. Annotations predicted 13 329 coding genes and 169 non-coding RNAs. The genome sequencing data submitted to the National Microbiology Science Data Center numbered NMDC60016264, of which 13 053, 8 422, 8 460, 7 714 and 2 847 genes can be matched with the annotation information in NR, KEGG, KOG, GO and CAZy databases respectively. According to comparative genomics analysis, Stachybotrys is conservative, with core genes accounting for 71.44% of the total gene families. S. longispora FG216 and S. chlorohalonata IBT 40285 had the highest similarity. At the same time, 101 secondary metabolite synthesis gene clusters were predicted, among them 18 gene clusters matched the known compounds. Under the antiSMASH predicts that Cluster 57 is a gene cluster encoding the synthesis of the parent nuclear structure of FGFC1 isoindolinone, and the similarity of the gene cluster with S. chlorohalonata IBT 40285 is 40%. [Conclusion] The genome information of the rare marine fungus S. longispora FG216 has been uploaded to the National Microbial Science Data Center for public use, which provides important reference for the study of Stachybotrys species. Cluster 57 was also found to be the partial encoding gene of the parent nucleus of the fibrinolytic active compound FGFC1, a secondary metabolite of S. longispora FG216.