Genetic Diversity of Mop-top Virus: An Emerging Threat to the US Potato Production
Primary author: Ying Zhai
Primary college/unit: Agricultural, Human and Natural Resource Sciences
Potato mop-top virus (PMTV; Genus: Pomovirus; Family: Virgaviridae), a soil-borne RNA Virus, is an emerging threat to potato production in the US. PMTV is known to exist as two distinct strains; however, there is limited information on the population structure, strain incidence and distribution in the U.S. The complete genome of six isolates of PMTV collected from three states in the USA were sequenced, analyzed, and compared with a previously characterized isolate from Washington and all known PMTV sequences available in GenBank.
Genome-wide nucleotide sequence identities of the U.S. isolates ranged from 96% to 100%. Based on the coat protein amino acid sequence, all the U.S. isolates clustered with known severe (S) strains. Genetic diversity test showed that the S strain to be more diverse than the mild (M) strain and the PMTV recombinant strain. Population selection analysis revealed that most of the codons were generally negatively selected in the PMTV isolates studied. However, positive selection was detected at codon 689 in the RT domain, which could be an adaptation to facilitate vector transmission and to overcome host plant resistance.
The sequence characteristics and the observed genetic diversity would be useful in developing improved virus diagnostics to detect the virus in aerial plant parts, tubers, soil and the soil-borne vector.