Biomics

Our studies and others’ reveal ambiguity in the species identification of isolates with traditional phylogenetic markers – 16S rRNA gene DNA sequence and the intergenic spacer ITS1. This ambiguity is also observed in the use of DNA sequences of gene sets, most of which have evolved independently and have their own evolutionary history. Applying the tests recommended within the genomic taxonomy of microbes, alongside whole genome DNA sequencing, has shown that evaluations of strains’ taxonomic positions depend on the type of whole genome data used, as related to the core and variable pangenome component. In addition, the number of deciphered reference genomes is limited for a sufficiently large number of taxonomic group members, making species identification incomplete at minimum. The discussed observations demonstrate the lack of a unified genetic system for species identification of isolates (as well as for prokaryote species classification itself), which justifies the use of the polyphasic approach in their systematics, combining traditional molecular genetic tests with phenotypic traits of strains. These tests, as a rule, use phylogenetic markers from the core pangenome component. They reflect only part of the evolution history of the organisms (somewhat limited in time), without allowance for horizontal gene transfer. The latter can be decisive in the acquisition of various traits by prokaryotes, which help them live in specific ecological niches and are crucial to species identification.

prokaryotes, genetic systematics, rhizosphere microflora, taxonomic studies, whole genome DNA sequencing, genomic taxonomy of microbes, microbial genomic taxonomy, polyphasic approach

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