枯草芽孢杆菌N2-10的基因组测序和比较基因组分析

Genome sequencing and comparative genomics analysis of Bacillus subtilis N2-10

摘要:

【背景】枯草芽孢杆菌N2-10是一株具有较强抑菌能力且能产纤维素酶等多种水解酶的革兰氏阳性菌，在发酵饲料中具有较大的应用潜力。【目的】通过获得枯草芽孢杆菌N2-10的全基因组序列信息，进一步解析菌株次级代谢产物合成基因信息，并通过比较基因组学分析菌株N2-10与模式菌株的差异性，为阐明N2-10抑菌和益生机制提供理论基础。【方法】通过二代Illumina NovaSeq联合三代PacBio Sequel测序平台，对菌株N2-10进行全基因组测序，将测序数据进行基因组组装、基因预测与功能注释，并利用比较基因组学分析N2-10与其他菌株的差异。【结果】菌株N2-10基因组大小为4036899bp，GC含量为43.88%；共编码4163个编码基因，所有编码基因总长度为3594369bp，编码区总长度占基因组总长度的89.04%；含有85个tRNA、10个5S rRNA、10个16S rRNA、10个23S rRNA，以及2个CRISPR-Cas、1个前噬菌体和6个基因岛；在GO(gene ontolog)、COG(clusters of orthologous groups of protein)、KEGG(Kyoto encyclopedia of genes and genome)、CAZy(carbohydrate-active enzyme)数据库中分别注释到3048、3177、3894、145个基因；此外，菌株N2-10共注释到10个次级代谢产物合成基因簇，包括根霉素A、表面活性素、bacillaene、丰原素、儿茶酸铁载体杆菌苷、芽孢杆菌素A、溶杆菌素生物合成基因簇和3个未知基因簇；比较基因组分析结果表明，菌株N2-10与模式菌株枯草芽孢杆菌168具有较高相似性。【结论】通过全基因组测序技术揭示了菌株N2-10的遗传信息，为深入了解N2-10产生多种次级代谢产物提供了参考，为进一步开发利用N2-10提供了坚实有力的依据。

Abstract:

[Background] With strong bacteriostatic activity, Gram-positive Bacillus subtilis N2-10 produces diverse hydrolases such as cellulase, thus showing huge potential in feed fermentation. [Objective] The whole genome of N2-10 was sequenced and the genes related to the synthesis of the secondary metabolites were analyzed. Based on comparative genomics, the difference between N2-10 and the model strain was dissected. The findings are expected to lay a theoretical basis for clarifying the bacteriostatic and probiotic mechanisms of this strain. [Methods] The genome of N2-10 was sequenced by Illumina NovaSeq and PacBioSequel, followed by genome assembly, gene prediction, and functional annotation. The differences between N2-10 and a model strain were analyzed by comparative genomics. [Results] The genome of N2-10 is 4 036 899 bp, with GC content of 43.88%. It has 4 163 coding genes with the total length of 3 594 369 bp, and the total length of the coding region accounts for 89.1% of the total genome length. In detail, it has 85 tRNA genes, 10 5S rRNA genes, 10 16S rRNA genes, 10 23S rRNA genes, 2 CRISPR-Cas sequences, and 6 gene islands. Moreover, this strain was also found to have a prophage. In addition, 3 048, 3 177, 3 894, and 145 genes were annotated in GO (gene ontolog), COG (clusters of orthologous groups of proteins), KEGG (Kyoto encyclopedia of genes and genomes), and CAZy (carbohydrate-active enzymes) databases, respectively. At the same time, 10 gene clusters for the synthesis of secondary metabolites were predicted, including biosynthesis gene clusters rhizocticin A, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin and 3 unknown gene clusters. Comparative genomics analysis showed that N2-10 had high homology with B. subtilis 168. [Conclusion] Through genome sequencing, we unveiled the genetic information of N2-10, providing a reference for further understanding the secondary metabolites of this stain and further development and utilization of it.