Journal
VIRUS GENES
Volume 58, Issue 1, Pages 42-52Publisher
SPRINGER
DOI: 10.1007/s11262-021-01875-4
Keywords
Tobacco rattle virus; Virgaviridae; Tobravirus; Potato virus; Genetic diversity; Evolution; RNA virus; Recombination
Categories
Funding
- USDA-NIFA-SCRI [2014-51181-22373]
- USDA National Institute of Food and Agriculture, Hatch project [1016563]
- Graduate Program in Molecular Plant Sciences
- Department of Plant Pathology at Washington State University (WSU), Pullman, WA, USA
- NIFA [687378, 2014-51181-22373] Funding Source: Federal RePORTER
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TRV, an important soil-borne virus of potato transmitted by nematodes, shows genetic clustering among isolates from different potato-growing regions in the USA, with low genetic diversity among American isolates and less constraint on the 1b gene. Phylogenetic incongruence between RNA1 and RNA2 segments indicates different evolutionary lineages.
Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.
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