Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces

Abstract

Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived Streptomyces harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived Streptomyces have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine Streptomyces and developing their secondary metabolites in the future.

Keywords: Streptomyces; biosynthetic gene clusters; comparative genomics; ecotype; phylotype; secondary metabolites.

Figure 1

Genomic size and gene counts of Streptomyces derived from various marine environments.

Figure 2

Secondary metabolism biosynthetic gene clusters (SMBGC) category counts identified in marine Streptomyces genomes.

Figure 3

Individual and exclusive orthologous clusters (OCs) of marine Streptomyces genomes.

Figure 4

Maximum-likelihood phylogenomic tree based on the concatenation of 888 single-copy OC proteins shared by all of marine Streptomyces. Filled circle indicated nodes showing >85 of bootstrap values. Kitasatospora setae KM-6054 was used as an outgroup.

Figure 5

Heat maps of clade-specific SMBGCs. Dark brown and light brown indicate presence and absence of SMBGCs.

Figure 6

Distribution percentages of ecotype-specific SMBGCs.