Time - the emerging dimension of plant virus studies

Abstract

Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations. Most of these viruses have single-stranded positive-sense RNA genomes, but a few have single-stranded DNA genomes. The studies show that extant populations of these viral species are only decades to centuries old. The genera in which they are placed have diverged since agriculture was invented and spread around the world during the Holocene period. We suggest that this is not mere coincidence but evidence that the conditions generated by agriculture during this era have favoured particular viruses. There is also evidence, albeit less certain, that some plant viruses, including a few shown to have measurably evolving populations, have much more ancient origins. We discuss the possible reasons for this clear discordance between short-and long-term evolutionary rate estimates and how it might result from a large timescale dependence of the evolutionary rates. We also discuss briefly why it is useful to know the rates of evolution of plant viruses.

Genus-Specific Substitution Rate Variability among Picornaviruses

“…Among the veterinary picornaviruses, three aphthovirus serotypes (FMDV-A, -C, and -O) still evolve significantly more slowly than the enterovirus serotype (SVDV). This serotype-to-serotype comparison confirms that the higher evolutionary rates of enteroviruses are not solely due to a difference in taxonomic scale (20).…”

“…The assumption that family members have identical rates underlies the recent estimations of long-term evolutionary rates of whole viral families, including those of the Luteoviridae (51), Potyviridae (20), and sobemoviruses (14). Our results discourage the continued presumption that evolutionary-rate differences among related genera or species must be negligible.…”

Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

“…In California, nucleotide diversity of Cucumber mosaic virus, CTV, and Citrus psorosis virus have been estimated as ≈0. 030 (31,34,46), which is also low in comparison with bacteriophages, animal viruses, and some plant viruses (14,20).…”

“…Like many animal viruses and bacteriophages, some RNA plant viruses have measurably evolving populations (11,20) whereas others evolve more slowly and have genetically stable populations (19). Two key aspects affecting virus evolution are the means of spread and host type.…”

“…In California, nucleotide diversity of Cucumber mosaic virus, CTV, and Citrus psorosis virus have been estimated as ≈0. 030 (31,34,46), which is also low in comparison with bacteriophages, animal viruses, and some plant viruses (14,20).Genetic differentiation was evaluated with the statistical tests Ks*, Z*, and S nn , and the extent of genetic differentiation and, therefore, gene flow was estimated with the coefficient F st . When samples collected from the USDA Germplasm collection (located at UC Davis) were compared with the isolates collected from commercial fields in California, the F st value was equal to -0.021 and the three statistical tests were nonsignificant.…”