Profiling of Genes Related to Cross Protection and Competition for NbTOM1 by HLSV and TMV

10.1371/journal.pone.0073725PLoS ONE89-POLN

The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture

Background: Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other. Methods and Findings: We have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas. Conclusions/Significance: Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.1561024 nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation

Strain-induced stripe phase in charge-ordered single layer NbSe2

Charge density waves are ubiquitous phenomena in metallic transition metal dichalcogenides. In NbSe2, a triangular 3x3 structural modulation is coupled to a charge modulation. Recent experiments reported evidence for a triangular-stripe transition at the surface, due to strain or accidental doping and associated to a 4x4 modulation. We employ ab initio calculations to investigate the strain-induced structural instabilities in a pristine single layer and analyse the energy hierarchy of the structural and charge modulations. Our results support the observation of phase separation between triangular and stripe phases in 1H-NbSe2, relating the stripe phase to compressive isotropic strain, favouring the 4x4 modulation. The observed wavelength of the charge modulation is also reproduced with a good accuracy