一株分离自运城盐湖土壤沉积物的链霉菌(Streptomyces sp.) YH02全基因组测序和比较基因组特征

Whole genome sequencing and comparative genomic analysis of Streptomyces sp. YH02 isolated from the soil sediment in Yuncheng Salt Lake

摘要:

目的 链霉菌(Streptomyces sp.) YH02是从山西运城盐湖土壤沉积物中分离的一株革兰氏阳性放线菌。解析菌株YH02的全基因组序列信息，探究其在种属进化关系中的位置，深入挖掘其次级代谢产物基因资源。方法 利用Illumina和PacBio平台相结合的测序技术对菌株YH02进行全基因组测序，并进行基因预测、功能注释、次级代谢产物合成基因簇预测、比较基因组学分析以及形态和生理生化测定。结果 菌株YH02基因组为一条线性染色体，全长8 285 116 bp，G+C含量为71.77%，编码7 237个开放阅读框；在GO、COG、KEGG、CAZy数据库中分别注释到2 829、5 478、4 805、279个基因；蛋白亚细胞定位分析预测到多种分泌系统相关蛋白和1 030个转运蛋白；同时预测到菌株YH02中存在32个次级代谢产物合成基因簇，涉及萜烯类、非核糖体肽类、聚酮类、核糖体合成和翻译后修饰肽类等多种天然产物的合成。比较基因组学分析揭示了15 739个泛基因组直系同源基因簇和4 267个核心基因组直系同源基因簇。基于16S rRNA基因序列的系统发育树分析显示，菌株YH02与委内瑞拉链霉菌(Streptomyces venezuelae) ATCC 10712、沙阿霉素链霉菌(Streptomyces zaomyceticus) NBC 00278亲缘关系较近，但平均核苷酸一致性(average nucleotide identity, ANI)分析小于95.00%，数字DNA-DNA杂交(digital DNA-DNA hybridization, dDDH)值小于70.00%。形态学和生理生化特性分析表明，菌株YH02在ISP 2培养基上的气生菌丝体呈现浅粉色，其对pH值、氯化钠耐受量和生长温度的耐受性与近缘菌株存在差异，且在淀粉水解能力上表现出较弱的活性，同时具有明胶液化、硝酸盐还原阳性、牛奶凝固缓慢的特性。结论 基于基因组学和生理生化特性的分析结果，菌株YH02被确认为链霉菌属潜在新种。本研究不仅丰富了微生物物种资源库，而且为探索具有独特作用机制的天然产物提供了理论基础和潜在的遗传资源。

Abstract:

Objective To elucidate the phylogenetic position and mine the gene resources for synthesis of secondary metabolites from Streptomyces sp. YH02, a Gram-positive actinomycete strain isolated from the soil sediment of Yuncheng Salt Lake in Shanxi.Methods Illumina and PacBio platforms were used for whole genome sequencing of YH02, which was followed by gene prediction, functional annotation, prediction of secondary metabolite synthetic gene clusters (BGCs), comparative genomic analysis, and morphological, physiological, and biochemical characterization.Results The YH02 genome was a linear chromosome spanning 8 285 116 bp, with the G+C content of 71.77% and 7 237 open reading frames. Gene annotations in the GO, COG, KEGG, and CAZy identified 2 829, 5 478, 4 805, and 279 genes, respectively. The subcellular localization analysis predicted various secretion system-related proteins and 1 030 transporters. Additionally, 32 secondary metabolite BGCs were predicted in strain YH02, involving the synthesis of various natural products such as terpenoids, non-ribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides. The comparative genomic analysis revealed 15 739 pan-genome orthologous gene clusters and 4 267 core genome orthologous gene clusters. The phylogenetic analysis based on the 16S rRNA gene sequence revealed a proximate phylogenetic affiliation between strain YH02 and Streptomyces venezuelae ATCC 10712 as well as Streptomyces zaomyceticus NBC 00278. However, the average nucleotide identity (ANI) value was below the threshold of 95.00%, and the digital DNA-DNA hybridization (dDDH) value was less than 70.00%. YH02 exhibited light pink aerial mycelia on the ISP 2 medium. It showed significant differences in tolerance to pH, sodium chloride, and growth temperature compared with its closely related strains. Additionally, this strain demonstrated weak starch hydrolysis activity, positive gelatin liquefaction, positive nitrate reduction, and slow milk coagulation.Conclusion Based on the findings from genomic, physiological, and biochemical analyses, strain YH02 is confirmed as a potential new species of Streptomyces. This study not only enriches the microbial resource pool but also provides a theoretical basis and potential genetic resources for mining the natural products with unique mechanisms of action.