The epidemiology of yam viruses remains largely unexplored. We present a large-scale epidemiological study of yam viruses in Guadeloupe based on the analysis of 1124 leaf samples collected from yams and weeds. We addressed the prevalence of cucumber mosaic virus (CMV), Cordyline virus 1 (CoV1), Dioscorea mosaic associated virus (DMaV), yam asymptomatic virus 1 (YaV1), yam mosaic virus (YMV), yam mild mosaic virus (YMMV), badnaviruses, macluraviruses and potexviruses, and the key epidemiological drivers of these viruses. We provide evidence that several weeds are reservoirs of YMMV and that YMMV isolates infecting weeds cluster together with those infecting yams, pointing to the role of weeds in the epidemiology of YMMV. We report the occurrence of yam chlorotic necrosis virus (YCNV) in Guadeloupe, the introduction of YMMV isolates through the importation of yam tubers, and the absence of vertical transmission of YaV1. We identified specific effects on some cropping practices, such as weed management and the use of chemical pesticides, on the occurrence of a few viruses, but no crop-related factor had a strong or general effect on the overall epidemiology of the targeted viruses. Overall, our work provides insights into the epidemiology of yam viruses that will help design more efficient control strategies.
25Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of 26 their hosts and are signatures of viral infections that may have occurred millions of years ago. The 27 study of EVEs, coined paleovirology, provides important insights into virus evolution. The 28Caulimoviridae is the most common group of EVEs in plants, although their presence has often been 29 overlooked in plant genome studies. We have refined methods for the identification of caulimovirid 30EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced 31 flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the 32 most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which 33 represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one 34 and as many as five different caulimovirid genera were frequently detected, and florendoviruses 35 were the most widely distributed, followed by petuviruses. From the analysis of the distribution of 36 different caulimovirid genera within different plant species, we propose a working evolutionary 37 scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million 38 years ago) followed by vertical transmission and by several cross-division host swaps. 39 40 41peer-reviewed)
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