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. 2021 Nov 1;19(11):621.
doi: 10.3390/md19110621.

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

Pedro Albuquerque  1   2 , Inês Ribeiro  3   4 , Sofia Correia  3 , Ana Paula Mucha  3   5 , Paula Tamagnini  1   2   5 , Andreia Braga-Henriques  6   7 , Maria de Fátima Carvalho  3   4 , Marta V Mendes  1   2
Affiliations

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

Pedro Albuquerque et al. Mar Drugs. .

Abstract

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.

Keywords: Streptomyces; de novo assembly; deep-sea actinobacteria; genome mining; natural products.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Schematic representation of the chromosomes of isolates MA3_2.13 (a) and S07_1.15 (b) generated by DNAPlotter v 18.1.0. The chromosomes are represented as open circles and for S07_1.15, only the large contig is shown. From outside to inside, the concentric circles represent: genome coordinates, coding sequences (CDS) in the forward strain (in blue) and in the reverse strain (in green), regions of putative BGCs (in red), tRNA and rRNA genes (in cyan and in black, respectively); GC percentage plot with default settings (above average in olive and below average in purple).
Figure 2
Figure 2
WGS phylogenetic tree of 280 NCBI RefSeq Streptomyces strains and isolates MA3_2.13 and S07_1.15 (highlighted in bold), generated using the GToTree workflow and visualized with the web-based tool Interactive Tree of Life (https://itol.embl.de/ (accessed on 10 October 2021)). Portions of the tree collapsed are labelled and numbers represent the number of leaves/genomes in the collapsed subtrees. Strains name in blue indicate strains isolated from marine samples.
Figure 3
Figure 3
Occurrence of BGCs types in both strains as predicted by antiSMASH. Data were retrieved from Supplementary Tables S6 and S7.
See this image and copyright information in PMC

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