Reclassification of two Nocardiopsis species using whole genome analysis

Abstract

This study revisits the taxonomic classification of the genus Nocardiopsis through the application of advanced genome-based methodologies, representing a notable advancement beyond traditional approaches that primarily rely on 16S rRNA gene sequences and phenotypic traits. The advent of Next-Generation Sequencing (NGS) and sophisticated bioinformatic tools has enabled a more precise framework for prokaryotic classification. However, many recognized species still lack complete genome sequences. In this study, we employed overall genome-related indices (OGRI), particularly Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH), to reassess the phylogenetic relationships within the genus. Comparative analyses of complete 16S rRNA sequences demonstrated high genetic similarity between N. umidischolae 66/93 ^T and N. tropica VKMAc-1457 ^T (99.61% similarity), as well as between N. rhodophaea JCM15313^T and N. rosea JCM15314^T (100% identity). The dDDH, ANI%, FastANI%, ANIm, and ANIb values further supported these results, with 73.2%, 96.94%, 96.15%, 97.19%, and 96.74% for the former pair, and 93.6%, 99.13%, 99.97%, 99.98%, and 99.27% for the latter pair, respectively. All values surpassed the species delineation thresholds of 70% for dDDH and 95–96% for ANI. Consequently, we propose reclassifying N. umidischolae as a heterotypic synonym of N. tropica, and N. rosea as a heterotypic synonym of N. rhodophaea, in accordance with the International Code of Nomenclature of Prokaryotes (ICNP).