Abstract
Actinobacteria are prokaryotes with a large biotechnological interest due to their ability to produce secondary metabolites, produced by two main biosynthetic gene clusters (BGCs): polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Most studies on bioactive products have been carried out on actinobacteria isolated from soil, freshwater or marine habitats, while very few have been focused on halophilic actinobacteria isolated from extreme environments. In this study we have carried out a comparative genomic analysis of the actinobacterial genus Saccharomonospora, which includes species isolated from soils, lake sediments, marine or hypersaline habitats. A total of 19 genome sequences of members of Saccharomonospora were retrieved and analyzed. We compared the 16S rRNA gene-based phylogeny of this genus with evolutionary relationships inferred using a phylogenomic approach obtaining almost identical topologies between both strategies. This method allowed us to unequivocally assign strains into species and to identify some taxonomic relationships that need to be revised. Our study supports a recent speciation event occurring between Saccharomonospora halophila and Saccharomonospora iraqiensis. Concerning the identification of BGCs, a total of 18 different types of BGCs were detected in the analyzed genomes of Saccharomonospora, including PKS, NRPS and hybrid clusters which might be able to synthetize 40 different putative products. In comparison to other genera of the Actinobacteria, members of the genus Saccharomonospora showed a high degree of novelty and diversity of BGCs.
Highlights
Actinobacteria are a diverse group of clinical, industrial and ecologically important bacteria known for their capacity to cause diseases as well as their potential to produce secondary metabolites widely used in a variety of fields, such as medicine, pharmacy, industrial microbiology and biotechnology, among others (Bérdy, 2012; Doroghazi and Metcalf, 2013)
A total of 19 genome sequences affiliated to members of the genus Saccharomonospora were retrieved from National Center for Biotechnology Information (NCBI) GenBank (18 genomes) and from Joint Genome Institute (JGI) (1 genome) databases, 12 of which belong to type strains of species or subspecies within this genus, and the remaining seven were not affiliated to any particular species or subspecies (Table 1)
The draft genome of Saccharomonospora iraqiensis subsp. iraqiensis IQ-H1T was named as Actinopolyspora iraqinesis IQ-H1T in GenBank database but it was included in this study since both names are homotypic synonyms
Summary
Actinobacteria are a diverse group of clinical, industrial and ecologically important bacteria known for their capacity to cause diseases as well as their potential to produce secondary metabolites widely used in a variety of fields, such as medicine, pharmacy, industrial microbiology and biotechnology, among others (Bérdy, 2012; Doroghazi and Metcalf, 2013). Genes involved in secondary metabolite production are commonly grouped within the genome and are usually known as biosynthetic gene clusters (BGCs) (Osbourn, 2010). Biosynthetic gene clusters for secondary metabolites have been studied in actinobacteria isolated from different environments, such as soil (Sharma et al, 2016; Wang et al, 2018), caves (Gosse et al, 2019), freshwater (Zothanpuia et al, 2018), marine (Zhang et al, 2019; Ishaque et al, 2020) and as endophytes from plants (Passari et al, 2016, 2017). Halophilic actinobacteria from extreme ecosystems have been reported, but only biosynthetic gene clusters from Actinopolyspora erythraea YIM 90600T have been located and identified so far (Chen et al, 2014; Corral et al, 2020)
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