Phylogenetic Analysis of Poxviridae Genomes Using K-mer Approach

Tatyana Nepomnyashchikh¹, Denis Antonets², Tatyana Tregubchak³, Alexander Shvalov⁴, Elena Gavrilova⁵, Rinat Maksyutov^6
1SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, nepom@vector.nsc.ru
²SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, antonec@yandex.ru
³SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, tregubchak_tv@vector.nsc.ru
⁴SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, shvalov_an@vector.nsc.ru
⁵SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, gavrilova_ev@vector.nsc.ru
⁶SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, maksyutov_ra@vector.nsc.ru

Abstract There is a growing interest towards alignment-free approaches that use k-mers as genomic features. Large sizes of poxvirus genomes, their complex organization with repetitive regions and recombination sites, makes it difficult to produce accurate whole genome alignments especially for distantly related species. K-mer based trees built for 663 whole genome sequences were found to be in good agreement with alignment-based ones and correspond well to currently accepted taxonomy and evolution of poxviruses.