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

作　　者：李珍华 王佳欣 张琳婕 孙宇佳 田蓉 杨瑾 刘缙[1] LI Zhenhua;WANG Jiaxin;ZHANG Linjie;SUN Yujia;TIAN Rong;YANG Jin;LIU Jin(Life Sciences Department,Yuncheng University,Yuncheng,Shanxi,China)

机构地区：[1]运城学院生命科学系,山西运城

出　　处：《微生物学报》2025年第3期1053-1069,共17页Acta Microbiologica Sinica

基　　金：山西省基础研究计划(自由探索类)(20210302124526,202203021212176);山西省高等学校科技创新项目(2021L472);运城学院博士科研启动项目(YQ-2020027)。

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Pac Bio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 r RNA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) ATCC10712、沙阿霉素链霉菌(Streptomyceszaomyceticus)NBC00278亲缘关系较近,但平均核苷酸一致性(averagenucleotideidentity, ANI)分析小于95.00%,数字DNA-DNA杂交(digitalDNA-DNAhybridization,d DDH)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p H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[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]Ilumina 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 8285116 bp,with the G+C content of 71.77%and 7237 open reading frames.Gene annotations in the GO,COG,KEGG,and CAZy identified 2829,5478,4805,and 279 genes,respectively.The subcellular localization analysis predicted various secretion system-related proteins and 1030 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 15739 pan-genome orthologous gene clusters and 4267 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 bi

关 键 词：链霉菌 全基因组测序 次级代谢合成基因簇 比较基因组 

分 类 号：S154.3[农业科学—土壤学]