小串链霉菌XG40全基因组测序及序列分析

Whole-genome Sequencing and Analysis of Streptomyces catenulae XG40

小串链霉菌(Streptomyces catenulae)XG40是一株对蜜柚黑斑病等真菌病害具有较好拮抗作用的生防放线菌。本研究通过第三代PacBio全基因组测序平台,对小串链霉菌XG40进行全基因组测序和分析,共获得3个contigs,包含1个染色体DNA和2个质粒DNA,其基因组全长为9772324 bp,GC含量为70.58%,蛋白编码基因8074个,占整个基因组的96.41%。利用antiSMASH软件,预测到46个次级代谢产物合成基因簇,其中包含聚酮合成酶(PKS)和非核糖体肽合成酶(NRPS)的基因簇共有24个,占总基因簇数量的52.17%。有7个基因簇与已知基因簇(desferrioxamin B、pristinol、Neoantimyci、2-methylisoborneol、nigericin、ectoine、geosmin)的相似性为100%,4个基因簇与已知基因簇(miharamycin A/B、SW-163C/E/F/G/UK-63598、gilvocarcin V、coelibactin)的相似性在80%以上,比较分析发现该菌株具备一定的合成尼日菌素和褐黄癌菌素V等抗菌物质的能力。共线性分析表明XG40与根霉链霉菌(S.rhizosphaericus)DSM41760、马来西亚链霉菌(S.malaysiensis)DSM14702、黑孢链霉菌(S.melanosporofaciens)DSM 40318和(S.himastatinicus)ATCC 53653四株链霉基因组之间存在插入和缺失、倒位、易位等基因组重排事件。该研究结果为深入挖掘XG40生防潜力,开发可用于农业生物防治的次级代谢产物提供理论基础。

Streptomyces catenulae XG40 is a biocontrol strain with antagonism to pathogens of pomelo black spot.In this study,the whole-genome sequence of S.catenulae XG40 was completed by the third generation sequencing plat-form PacBio Sequel.Three contigs were obtained,including one chromosomal DNA and two plasmid DNA.The total length of the genome sequencing was 9772324 bp with 70.58%GC content,and 8074 protein-coding genes were pre-dicted which were accounted for 96.41%of all genes.Forty-six putative secondary metabolite biosynthetic gene clusters were found in the genome using the online antiSMASH software,among twenty-four PKS and NRPS,which were ac-counted for 52.17%of all gene clusters.Seven putative gene clusters showed 100%similarities to known gene clusters:desferrioxamin B,pristinol,neoantimyci,2-methylisoborneol,nigericin,ectoine,geosmin gene clusters.Four putative gene clusters showed more than 80%similarities to known gene clusters:miharamycin A/B,SW-163C/E/F/G/UK-63598,gilvocarcin V,coelibactin.Clusters analysis showed that S.catenulae XG40 had certain ability of the biosynthesis of nigericin and gilvocarcin V with antibacterial activity.The analysis of synteny indicated that genome insertion,deletion,rearrangement and translocation happened among the genomes of S.catenulae XG40,S.rhizosphaericus DSM 41760,S.malaysiensis DSM 14702,melanosporofaciens DSM 40318 and S.himastatinicus ATCC 53653.This research would provide a theoretical basis for further discovering biocontrol potential of XG40 and the secondary metabolites for agri-cultural biological control.