Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation

• Published in: Research in microbiology 2023-03, Vol.174 (3), p.103998-103998, Article 103998
• Main Authors: Santos, Roselane Gonçalves dos, Hurtado, Raquel, Rodrigues, Diego Lucas Neres, Lima, Alessandra, dos Anjos, William Ferreira, Rifici, Claudia, Attili, Anna Rita, Tiwari, Sandeep, Jaiswal, Arun Kumar, Spier, Sharon J., Mazzullo, Giuseppe, Morais-Rodrigues, Francielly, Gomide, Anne Cybelle Pinto, de Jesus, Luís Cláudio Lima, Aburjaile, Flavia Figueira, Brenig, Bertram, Cuteri, Vincenzo, Castro, Thiago Luiz de Paula, Seyffert, Núbia, Santos, Anderson, Góes-Neto, Aristóteles, de Jesus Sousa, Thiago, Azevedo, Vasco
• Format: Article
• Language: English
• Subjects: Actinomycetales - genetics; Base Sequence; Comparative genomics; Core genome; Dietzia; Genome, Bacterial - genetics; Genomics; Pangenome; Phylogenetics; Phylogenomic; Phylogeny; Reassign species; Sequence Analysis, DNA
• ISSN: 0923-2508; 1769-7123
• DOI: 10.1016/j.resmic.2022.103998

Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.