Abstract
The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111T. The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.
Highlights
The genus Nocardiopsis is affiliated with the phylum Actinobacteria, which is marked by being Gram-positive and having a genome with a high guanine and cytosine (G+C) content
Various hypotheses argue that genome size is itself subject to natural selection, i.e., the tight packing and small sizes of bacterial genomes is an adaptation for reproductive efficiency or competitiveness [31]
Nocardiopsis is a group of widely-distributed actinobacteria that can populate quite varied ecological niches with differences in nutrients, osmotic pressure, pH, temperature, and the presence of toxic molecules
Summary
The genus Nocardiopsis is affiliated with the phylum Actinobacteria, which is marked by being Gram-positive and having a genome with a high guanine and cytosine (G+C) content. This unique group has previously received attention because of the pathogenicity of the type species, N. dassonvillei subsp. The genus is of interest for both its ecological versatility and its ability to produce a rich array of bioactive metabolites. Members of the genus produce such bioactive metabolites as methylpendolmycin [6], apoptolidin [7], griseusin D [8], lipopeptide biosurfactants [9], thiopeptides [10] and naphthospironone A [11]. The outstanding and diverse physiological traits of microbial populations can be attributed to their underlying genetic diversity and their mechanisms of generating genetic variation
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