生防菌解淀粉芽孢杆菌 SQ-2 全基因组测序及生物信息学分析

Whole genome sequencing and genomics analysis of Bacillus amyloliquefaciens SQ-2 with biocontrol activity

摘要:

【背景】解淀粉芽孢杆菌SQ-2是从市售豆瓣酱中分离得到的一株益生菌，实验表明菌株SQ-2具有较强的抑制植物病原真菌的能力，说明SQ-2具有较好的生物防治能力，有作为生物农药的潜力。【目的】研究菌株SQ-2的遗传信息并揭示其抑菌机制。【方法】在Illumina MiSeq X10平台上对菌株SQ-2进行全基因组测序，使用Trim Galore v.0.4.0清理原始数据，并使用FastQC检查质量；使用SOAPdenovo2进行从头组装，使用antiSMASH鉴定负责次级代谢产物生物合成的基因。【结果】解淀粉芽孢杆菌SQ-2基因组大小为3 486 537 bp，GC含量为46.63%，共编码4 298个基因，共发现11个与次级代谢产物生物合成相关的基因簇，其中6个被确定为抗真菌物质合成簇，分别编码bacillaene、bacilysin、butirosin、fengycin、bacillibactin和surfactin。基因组框架测序数据提交至NCBI获得GenBank登录号为JAHXSB000000000。超高液相色谱/质谱联用分析表明产生了儿茶酚型嗜铁素、多烯类和表面活性肽。【结论】获得了解淀粉芽孢杆菌SQ-2的基因组序列，该菌株对植物致病真菌具有强烈的拮抗活性。全基因组序列研究有助于对已知抗菌肽的利用及寻找新型抗真菌物质。

Abstract:

[Background] Bacillus amyloliquefaciens SQ-2 is a probiotic strain isolated from commercially available watercress paste, with previous experiments demonstrating its exceptional bacteriostatic ability against plant pathogenic fungi, indicative of strain SQ-2’s rather good bio-control abilities and potential application prospects in bio-pesticides. [Objective] To explore the genetic information of B. amyloliquefaciens SQ-2, and divulge its antifungal mechanism. [Methods] The whole-genome sequencing of strain SQ-2 was performed on an Illumina MiSeqX10 platform. Raw data were cleaned using Trim Galore v.0.4.0 and examined for quality using FastQC. In addition, de novo assembly was performed using the SOAPdenovo2 package. Genes responsible for the biosynthesis of secondary metabolites were identified using antiSMASH. [Results] The genome of B. amyloliquefaciens SQ-2 was 3 486 537 bp with the average guanine/cytosine (GC) content of 46.63%, which potentially coded 4298 genes. Eleven gene clusters related to secondary metabolite biosynthesis were discovered, of which six were identified as antifungal synthesis clusters, encoding bacillaene, bacilysin, butirosin, fengycin, bacillibactin, and surfactin, respectively. The sequencing data from this article were submitted to the NCBI and were available in the GenBank database (Login No. JAHXSB000000000). Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis indicated that the surfactin, bacillibactin, and bacillaene were produced by strain SQ-2. [Conclusion] This study presents the genome sequence of B. amyloliquefaciens SQ-2, and it exhibits intense antagonistic activity against plant pathogenic fungi. The entirety of this genome sequencing study can assist in utilizing known antifungal peptides and searching for novel antifungal substances to combat pathogens.