Using multiplex virtual PCR for genetic barcoding of \emph{Tequatrovirus} bacteriophages

O. Y. Kiryanova ; S. S. Kiselev ; V. V. Panyukov ; N. A. Nikulin ; N. N. Nazipova ; A. V. Chemeris ; A. A. Zimin

Matematičeskaâ biologiâ i bioinformatika, Tome 19 (2024) no. 2, pp. 369-392.

Résumé

In this paper, we investigate the possibility of using the multiplex virtual PCR method to develop approaches to barcoding the genomes of T4-type bacteriophages. A comparison of the multiplex virtual PCR method and phylogenomic analysis based on alignment-free approach was performed. A dataset of Tequatrovirus genomes previously selected for pangenomic analysis was used for this study. The genomes used were preliminarily checked for their adequate annotation and, accordingly, sequencing accuracy. A study using the multiplex virtual PCR method was carried out for 67 genomes, barcodes were generated, and similarity parameters were determined. Based on the obtained data, a phylogenetic tree was constructed using the neighbor joining method. For the same set of Straboviridae bacteriophage genomes, a phylogenomic tree was constructed based on pairwise distance matriх between oligonucleotide 10-mer sets. Comparison of these two trees showed differences in branching between the control distantly related genomes from the genera Mosigvirus and Dhakavirus, and the branch of the genomes of bacteriophages of the genus Tequatrovirus. The authors of the work suggested that these differences may reflect the features of the multiplex virtual PCR method, which is more applicable for assessing the similarity of closely related genomes than within genomes with an identity degree of less than 75%. It can be concluded that the multiplex virtual PCR method allows one to distinguish taxonomic groups of large bacteriophages, which include T4-type bacteriophages, at the genus level. Thus, using this method, within the genus of such bacteriophages one can more accurately compare the genomes of viruses with a length of about 170 kb. From a practical point of view, multiplex virtual PCR is quite applicable for including barcodes compiled on its basis in the bacteriophage passport for use in the practice of phage therapy.