来自南极洲类诺卡氏菌(Nocardioides sp.)InS609-2的全基因组序列分析

Whole-genome sequence analysis of Nocardioides sp.InS609-2 isolated from Antarctica

【背景】类诺卡氏菌(Nocardioides sp.)InS609-2是一株分离自南极洲罗斯海特拉诺瓦湾的恩克斯堡岛土壤中潜在的极地放线菌新种。尚无研究报道Nocardioides sp.InS609-2的全基因组序列,缺少对其功能基因、代谢产物合成途径及比较基因组学等的研究。【目的】解析Nocardioides sp.InS609-2的基因组序列信息,以深入挖掘次级代谢产物基因资源。【方法】利用Illumina HiSeq高通量测序平台对菌株InS609-2进行全基因组完成图测序,使用相关软件对测序数据进行基因组组装、基因预测和功能注释、预测次级代谢产物合成基因簇和共线性分析等。【结果】基因组最后得到的总长度为4524052 bp,G+C含量为69.42%,预测到4656个基因、56个tRNA和6个rRNA。根据Nocardioides sp.InS609-2的全基因组测序结果,分别有3761、3052、1767、4134和2725个基因在COG、GO、KEGG、NR和Swiss-Prot数据库中提取到注释信息。同时,还预测得到19个次级代谢产物合成基因簇。基因组测序数据提交至NCBI获得GenBank登录号为CP060034。Nocardioides sp.InS609-2与N.dokdonensis CP015079、N.yefusunii CP034929、N.euryhalodurans CP038267、N.seonyuensis CP038436、N.daphniae CP038462和N.okcheonensis CP087710这6株基因组同源性比较高的类诺卡氏菌进行共线性分析和蛋白聚类分类分析,得到的结果是7个基因组间既有保守性又各自有独特性。七个基因组共有44个蛋白聚类簇。最后进行16S rRNA基因系统发育树、泛基因组、core基因组和基因组进化树分析,进一步挖掘了Nocardioidessp.InS609-2的基因组信息。【结论】从基因组层面上预测了Nocardioides sp.InS609-2的次级代谢产物的生物合成基因簇,为InS609-2的后续相关研究提供了参考信息,具有重要意义。

[Background]Nocardioides sp.InS609-2 is a potential new strain of polar actinomycete isolated from the soil sample collected from Inexpressible Island in Terra Nova Bay of the Ross Sea,Antarctica.Little is known about the full genome sequence,functional genes,metabolite synthesis pathways,and comparative genomics of Nocardioides sp.InS609-2.[Objective]To explore the genes associated with secondary metabolites from the genome sequence of Nocardioides sp.InS609-2.[Methods]The complete genome map of InS609-2 was sequenced on the Illumina HiSeq platform,followed by read assembly,gene prediction,gene annotation,prediction of gene clusters for secondary metabolite biosynthesis,and synteny analysis.[Results]The full length of the genome was 4524052 bp,with the G+C content of 69.42%.A total of 4656 genes,56 tRNAs,and 6 rRNAs were predicted.Among them,3761,3052,1767,4134,and 2725 genes were annotated in COG,GO,KEGG,NR,and Swiss-Prot,respectively.Meanwhile,19 gene clusters for secondary metabolite synthesis were predicted.Genome sequencing data was submitted to NCBI,with the GenBank accession number CP060034.The synteny analysis and protein cluster analysis were performed for Nocardioides sp.InS609-2 together with N.dokdonensis CP015079,N.yefusunii CP034929,N.euryhalodurans CP038267,N.seonyuensis CP038436,N.daphniae CP038462,and N.okcheonensis CP087710.The results showed both conserved and unique regions among the seven genomes.The seven genomes shared 44 protein clusters.Finally,the 16S rRNA gene-based phylogenetic analysis,pan genome analysis,core genome analysis,and genome-based phylogenetic analysis were carried out to further mine the genomic information of Nocardioides sp.InS609-2.[Conclusion]This study provides reference information for predicting the gene clusters involved in secondary metabolite biosynthesis of Nocardioides sp.InS609-2 at the genomic level,which is essential for the subsequent studies of InS609-2.