植物内生链霉菌Streptomyces sp. SAT1的基因组测序和比较基因组分析

Genome sequencing and comparative genome analysis of Streptomyces sp. SAT1

摘要:

[背景] 一直以来，链霉菌都是活性物质的主要生产者，近年来随着抗生素滥用引起的环境和微生物抗药性问题越发严重，挖掘高效生物防治因子和新型抗生素成为了解决以上问题的重要手段。[目的] 通过获得植物内生链霉菌SAT1全基因组序列和次级代谢基因簇信息，利用比较基因组学和泛基因组学分析SAT1菌株的特殊性以及与其他链霉菌的共性，为阐明SAT1抑菌和内生机制提供理论基础，为揭示链霉菌的生态功能提供可靠数据。[方法] 通过三代测序平台PacBio Sequel完成SAT1基因组测序，利用生物信息学技术进行注释和功能基因分类；分别利用RAxML和PGAP软件进行系统发育树的构建和泛基因组分析；次级代谢基因簇的预测和分析通过antiSMASH网站完成。[结果] 获得SAT1菌株的全基因组完成图，该菌线性染色体长度约7.47 Mb，包含有4个质粒，GC含量近73%，共预测到7 550个蛋白编码基因，含有37个次级代谢基因簇，分属29个类型，其中默诺霉素基因簇与加纳链霉菌具有较高相似性。42株代表链霉菌中，单个菌株次级代谢基因簇数量为20-55个，主要类型为PKS类、Terpene类和Nrps类，而且含有大量杂合基因簇，各个菌株中特有基因数目较为庞大。[结论] 链霉菌SAT1菌株在基因组特点以及次级代谢基因簇的数量和类型上与其余41株链霉菌具有一定的共性，其中潮霉素B基因簇和默诺霉素基因簇合成的相关物质可能与SAT1抑菌活性密切相关。42株链霉菌中次级代谢基因簇数量的多少与基因组大小成正相关，同时大量杂合基因簇以及庞大的特有基因数目的存在说明链霉菌在长期进化过程中存在了很高程度的水平基因转移现象，可能具有重要的生态功能。

Abstract:

[Background] Streptomyces has always been the main producer of bioactive compounds. However, as the abusing of antibiotics, environmental pollution and drug resistance are becoming increasingly serious problem. The discovery of efficient bio-control factor and novel antibiotics becomes the main methods to solve these problems. [Objective] Obtain the whole genome sequence of the Streptomyces sp. SAT1 and the information about its secondary metabolite gene clusters; analyze the particularity and generality with other streptomycetes by the technology of comparative genomics and pan genomics. Form this, we could provide theoretical basis for illuminating the mechanism of bacteriostasis and growth-promoting in SAT1, and reliable data to reveal the ecological function of Streptomyces. [Methods] The sequence of SAT1 was completed by the third generation sequencing platform PacBio Sequel, then annotated and classified by bio-information technology; the software RAxML and PGAP was used to construct phylogenetic tree and analyze pan-genome, respectively. The prediction and analyze of the secondary metabolite gene clusters was achieved by antiSMASH. [Results] From the complete genome map of SAT1, the length of linear chromosome is 7.47 Mb, with 73% GC content, and four plasmids exist in the strain. Additionally, there are 7 550 genes which encoded proteins and 37 secondary metabolite gene clusters which classified by 29 types in SAT1. And the moenomycin gene cluster was highly homologous to Streptomyces ghanaesis ATCC14672 moenomycin gene cluster. In the 42 streptomycetes, it exists about 20-55 secondary metabolites gene clusters in each strain which classified into PKS, Terpene, Nrps and Heterozygous gene clusters. The dispensable genome was huge in these research objectives. [Conclusion] Streptomyces sp. SAT1 has many common points in the trait of genome and secondary gene clusters with other streptomycetes. We speculate the moenomycin and hygromycin_B gene clusters play an important role in the antibacterial activity of SAT1. In the 42 research objectives, the number of gene clusters and the size of genome has a positive correlation. In addition, the existence of abundant heterozygous gene clusters and large number of dispensable genome illustrate Streptomyces has high levels of horizon gene transfer over long periods of evolution, which possesses important environmental functions.