Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS

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.

Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov

“…The paraphyly of the genera Prauserella and Saccharomonospora was also observed by a similar study employing core-proteome analysis [16] and therefore the two genera Saccharomonospora and Prauserella should be merged as Saccharomonospora. However, when the phylogeny of the genera Prauserella and Saccharomonospora were evaluated via the GBDP approach using the TYGS webserver, the members of the genera Prauserella and Saccharomonospora were not monophyletic (Fig.…”

“…Salam et al [1] updated the reclassification in the phylum Actinobacteria based on concatenated universal protein marker gene sequence analysis and supported the transfer of the members of the family Actinopolysporaceae into the family Pseudonocardiaceae within the order Pseudonocardiales. Furthermore, in a recent comparative genomic analysis of the genus Saccharomonospora, the species Prauserella coralliicola and Prauserella endophytica were found to cluster very closely, but the taxonomic positions of P. coralliicola and P. endophytica were not resolved [16]. Additionally, the taxonomic opinion that Actinoalloteichus cyanogriseus and Streptomyces caeruleus are heterotypic synonyms and should be treated as belonging to a single species, Actinoalloteichus cyanogriseus, was not considered as validly published [17,18].…”

“…coralliicola and P. endophytica were not resolved [16]. Additionally, the taxonomic opinion that Actinoalloteichus cyanogriseus and Streptomyces caeruleus are heterotypic synonyms and should be treated as belonging to a single species, Actinoalloteichus cyanogriseus , was not considered as validly published [17, 18].…”

Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena

“…The evolutionary processes that lead to diversity, chromosomal dynamics, and rearrangement rates between species can be assessed by means of the analysis of the synteny among two or more genomes, that is, the spatial distribution of locally collinear blocks (Bhutkar et al, 2006). Thus, an approach to gain insight into the evolutionary distance between two species is to inspect the synteny of the genome sequences under study (Borriss et al, 2011;Ramírez-Durán et al, 2021). As indicated in the previous section, OGRI values equal to the species cutoffs were not able to reliably solve the taxonomic status of several species and so, the synteny analysis might shed light to elucidate the affiliation of those uncertain taxa.…”

“…In the post-genomic era, it is possible to take advantage of big genome databases and low-cost sequencing to infer phylogenetic relationships among prokaryotes using the core orthologous genes detected in the genomes under study in order to accurately elucidate their evolutionary history (de la Haba et al, 2019). Besides, comparative genomics and Overall Genome Related Indexes (OGRI) have been proposed as approaches to inspect the evolutionary distance among species and to delineate prokaryotic taxa at family, genus and species level (Borriss et al, 2011;Chun and Rainey, 2014;Konstantinidis et al, 2017;Ramírez-Durán et al, 2021) and current taxonomy should benefit from them.…”