Analysis of canna yellow streak virus complete genomes provides evidence of multiple intraspecies recombination events

Metatranscriptomic analysis of the canna (Canna spp., family Cannaceae) cv. ‘Krymskiy Samotzvet’ from the field collection of the Nikita Botanical Gardens, Yalta, Russia, was performed using the high-throughput sequencing on the Illumina HiSeq 2500 platform. The full-size genome of canna yellow streak virus (CaYSV, genus Potyvirus, family Potyviridae) was assembled using sequencing data. Analysis by the recombination detection program RDP4 of this new isolate along with 10 other CaYSV full-length genome sequences from the USA and the UK, available in GenBank, revealed at least four putative recombination events supported by statistically significant P-values. Three of them were found in the 3'-terminal part of the genomes. Five of the 11 isolates were identified as recombinants. No recombination was detected in the isolates NC1 to NC5 and BZ1 from the USA, suggesting that they may represent some “ancestral” forms of the CaYSV genome. Phylogenetic analysis of different genomic regions confirmed the results of recombination analysis. This is the first report of multiple recombination events among CaYSV isolates that may contribute to further understanding of the molecular variability and evolutionary history of this virus.