Data of genome assembly of the strain isolated from the livestock in Volga Region, Russian Federation.

are obligate intracellular bacteria globally widespread across humans, wildlife, and domesticated animals. is a primarily zoonotic pathogen with multiple hosts, which can be transmitted to humans, resulting in psittacosis or ornithosis. Since this pathogen is a well-recognized threat to human and animal health, it is critical to unravel in detail the genetic make-up of this microorganism. Though many genomes of have been studied to date, little is known about the variants of chlamydial organisms causing infection in Russian livestock. This research is the first genome assembly of the strain Rostinovo-70 of zoonotic origin that was isolated in Russian Federation. The results were obtained by using standard protocols of sequencing with the Illumina HiSeq 2500 and Oxford Nanopore MinION technology that generated 3.88 GB and 3.08 GB of raw data, respectively. The data obtained are available in NCBI DataBase (GenBank accession numbers are CP041038.1 & CP041039.1). The Multi-Locus Sequence Typing (MLST) showed that the strain Rostinovo-70 together with GR9 and C WS/RT/E30 belong to the sequence type (ST)28 that could be further separated into two different clades. Despite Rostinovo-70 and GR9 formed a single clade, the latter strain did not contain a cryptic plasmid characteristis to Rostinovo-70. Moreover, the genomes of two strains differed significantly in the cluster of 30 genes that in Rostinovo-70 were closer to rather than . The alignment of the genomes of and in this area revealed the exact boarders of homologous recombination that occurred between two Chlamydia species. These findings provide evidence for the first time of genetic exchange between closely related Chlamydia species.