桑氏链霉菌KJ40全基因组测序及分析

Whole-genome sequencing and analysis of Streptomyces sampsonii KJ40

摘要:

【背景】桑氏链霉菌(Streptomyces sampsonii) KJ40是一株具有防病、促生多重功能的放线菌，有作为生物农药的潜力。目前还没有相关研究报道S. sampsonii全基因组序列，这限制了其功能基因、代谢产物合成途径及比较基因组学等研究。【目的】解析S. sampsonii KJ40的基因组序列信息，以深入研究该菌株防病促生机制及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KJ40菌株进行全基因组测序，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、共线性分析等。【结果】基因组最后得到9个Scaffolds 和578个Contigs，总长度为7 261 502 bp，G+C%含量平均为73.41%，预测到6 605个基因、1 260个串联重复序列、804个小卫星序列、67个微卫星序列、90个tRNA、9个rRNA和19个sRNA。其中，2 429、3 765、2 890、6 063和1 911个基因分别能够在COG、GO、KEGG、NR和Swiss-Prot数据库提取到注释信息。同时，还预测得到21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：LORI00000000。S. sampsonii KJ40与Streptomyces coelicolor A3(2)、Streptomyces griseus subsp. griseus NBRC 13350三株链霉菌基因组存在翻转、易位等基因组重排，3个基因组共有1 711个蛋白聚类簇。【结论】研究为从基因组层面上解析KJ40菌株具有良好促生防病效果的内在原因提供基础数据，为深入了解链霉菌次级代谢合成途径提供参考信息，对S. sampsonii后续相关研究具有重要意义。

Abstract:

[Background] Streptomyces sampsonii KJ40 is an actinomycete with functions of disease prevention and promoting plant growth, it has the potential as a biological pesticide. However, there is no relevant study in the genome of S. sampsonii until now, limiting the research of its functional genes, metabolites synthesis pathway and comparative genomics etc. [Objective] To analyze the genome information of the S. sampsonii KJ40 strain, and to research the mechanism of functions of the strain, and its secondary metabolite genes. [Methods] The whole genome of KJ40 strain was sequenced on the Illumina HiSeq platform, and then sequenced reads were assembled, the genes were predicted, the gene annotation, secondary metabolite biosynthesis and synteny were also analyzed with softwares. [Results] In the whole genome, 9 scaffolds and 578 contigs were obtained. The total length was 7 261 502 bp, the average GC content was 73.41%. It contained 6 605 genes, 1 260 tandem repeat sequences, 804 minisatellite DNAs, 67 microsatellite DNAs, 90 tRNAs, 9 rRNAs, and 19 sRNAs. Among them, 2 429, 3 765, 2 890, 6 063 and 1 911 genes were able to annotate in COG, GO, KEGG, NR and Swiss-Prot databases respectively. 21 secondary metabolite biosynthetic gene clusters were also obtained. The sequencing data from this article are available in the GenBank database (accession number LORI00000000). There were 1 711 proteins clustered among S. sampsonii KJ40, Streptomyces coelicolor A3(2) and Streptomyces griseus subsp. griseus NBRC 13350. The analysis of synteny indicated that genome rearrangement and translocation happened among these genomes. [Conclusion] Our results show the genome information of KJ40 strain, it gives evidence that KJ40 is linked to disease prevention and promoting plant growth, and provided reference for understanding secondary metabolic synthesis pathway of Streptomyces, which is of great significance to the future research of S. sampsonii.