Bioinformatics and Computational Biology, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.
BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.
BMC Genomics. 2019 Dec 19;20(1):994. doi: 10.1186/s12864-019-6279-8.
Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays.
Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93-23, Streptomyces sp. 3211-3, and Streptomyces sp. S3-4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution.
Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93-23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.
链霉菌属中的细菌仍然是新天然产物发现的主要来源，并且作为农业中的土壤接种剂，它们可以促进植物生长并预防疾病。最近，链霉菌属被认为是天然抑制疾病土壤中的重要成员。为了更深入地了解抑制疾病的微生物群落的生态学和进化，我们对从抑制疾病的土壤中分离出的三种链霉菌菌株进行了基因组测序，并将其与以前测序的分离株进行了比较。用于测序的菌株在竞争或信号测定中表现出强烈的表型。
在这里，我们介绍了从抑制疾病的土壤中分离出的三种链霉菌菌株的从头测序，以产生高质量的完整基因组。链霉菌 GS93-23、链霉菌 3211-3 和链霉菌 S3-4 的线性染色体分别为 8.24 Mb、8.23 Mb 和大于 7.5 Mb。此外，其中两种菌株被发现具有大型线性质粒。每个菌株都拥有 26 到 38 个天然产物生物合成基因簇，与以前测序的链霉菌属相当。我们将这些新测序的基因组与以前测序的生物进行了比较。我们在密切相关的菌株之间看到了大量的天然产物生物合成多样性，而获得/失去染色体外 DNA 元件是基因组进化的主要驱动力。
长读测序数据为高 GC 链霉菌基因组的大片段组装提供了便利。虽然样本数量太少，无法得出明确的结论，但我们没有发现抑制疾病土壤分离物在生物合成基因簇数量方面具有特别优势的证据。GS93-23 与以前分离的链霉菌利迪希斯具有很强的序列相似性，这表明物种招募可能有助于抑制疾病的微生物群落的进化。
