Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.).

Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.

Epidemiology of Yam Viruses in Guadeloupe: Role of Cropping Practices and Seed-Tuber Supply.

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.

Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management.

Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.

Data on microsatellite markers in Colletotrichum gloeosporioides s.l., polymorphism levels and diversity range.

Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2-29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.

Varietal Dynamics and Yam Agro-Diversity Demonstrate Complex Trajectories Intersecting Farmers' Strategies, Networks, and Disease Experience.

Loss of varietal diversity is a worldwide challenge to crop species at risk for genetic erosion, while the loss of biological resources may hinder future breeding objectives. Loss of varieties has been mostly investigated in traditional agricultural systems where variety numbers are dramatically high, or for most economically important crop species for which comparison between pre-intensive and modern agriculture was possible. Varietal dynamics, i.e., turnover, or gains and losses of varieties by farmers, is nevertheless more rarely studied and while we currently have good estimates of genetic or varietal diversity for most crop species, we have less information as to how on farm agro-diversity changes and what cause its dynamics. We therefore investigated varietal dynamics in the agricultural yam system in the Caribbean island of Guadeloupe. We interviewed producers about varieties they cultivated in the past compared to their current varieties, in addition to characterizing yam cropping characteristics and both farm level and producers socio-economic features. We then used regression tree analyses to investigate the components of yam agro-diversity, varietal dynamics and impact of anthracnose on varieties. Our data demonstrated that no dramatic loss of varieties occurred within the last decades. Cultivation changes mostly affected widespread cultivars while frequency of uncommon varieties stayed relatively stable. Varietal dynamics nevertheless followed sub-regional patterns, and socio-economic influences such as producer age or farm crop diversity. Recurrent anthracnose epidemics since the 1970s did not alter varietal dynamics strongly, but sometimes translated into transition from Dioscorea alata to less susceptible species or into a decrease of yam cultivation. Factors affecting changes in agro-diversity were not relating to agronomy in our study, and surprisingly there were different processes delineating short term from long term varietal dynamics, independently of disease risk. Our results highlighted the importance of understanding varietal dynamics, an often overlooked component of agriculture sustainability, in addition to evolutionary forces shaping agro-diversity and genetic diversity distribution within crops. It is also crucial to understand how processes involved do scale up worldwide and for different crop species, so as not to mislead on-farm conservation efforts and efficacy of agro-diversity preservation.

Direct splash dispersal prevails over indirect and subsequent spread during rains in Colletotrichum gloeosporioides infecting yams.

Plant pathogens have evolved many dispersal mechanisms, using biotic or abiotic vectors or a combination of the two. Rain splash dispersal is known from a variety of fungi, and can be an efficient driver of crop epidemics, with infectious strains propagating rapidly among often genetically homogenous neighboring plants. Splashing is nevertheless a local dispersal process and spores taking the droplet ride seldom move farther than a few decimeters. In this study, we assessed rain splash dispersal of conidia of the yam anthracnose agent, Colletotrichum gloeosporioides, in an experimental setting using a rain simulator, with emphasis on the impact of soil contamination (i.e., effect of re-splashing events). Spores dispersed up to 50 cm from yam leaf inoculum sources, though with an exponential decrease with increasing distance. While few spores were dispersed via re-splash from spore-contaminated soil, the proportion deposited via this mechanism increased with increasing distance from the initial source. We found no soil contamination carryover from previous rains, suggesting that contamination via re-splashing from contaminated soils mainly occurred within single rains. We conclude that most dispersal occurs from direct splashing, with a weaker contribution of indirect dispersal via re-splash.

Optimal foraging predicts the ecology but not the evolution of host specialization in bacteriophages.

We explore the ability of optimal foraging theory to explain the observation among marine bacteriophages that host range appears to be negatively correlated with host abundance in the local marine environment. We modified Charnov's classic diet composition model to describe the ecological dynamics of the related generalist and specialist bacteriophages phiX174 and G4, and confirmed that specialist phages are ecologically favored only at high host densities. Our modified model accurately predicted the ecological dynamics of phage populations in laboratory microcosms, but had only limited success predicting evolutionary dynamics. We monitored evolution of attachment rate, the phenotype that governs diet breadth, in phage populations adapting to both low and high host density microcosms. Although generalist phiX174 populations evolved even broader diets at low host density, they did not show a tendency to evolve the predicted specialist foraging strategy at high host density. Similarly, specialist G4 populations were unable to evolve the predicted generalist foraging strategy at low host density. These results demonstrate that optimal foraging models developed to explain the behaviorally determined diets of predators may have only limited success predicting the genetically determined diets of bacteriophage, and that optimal foraging probably plays a smaller role than genetic constraints in the evolution of host specialization in bacteriophages.

Experimental estimate of the abundance and effects of nearly neutral mutations in the RNA virus phi 6.

Although the frequency and effects of neutral and nearly neutral mutations are critical to evolutionary patterns and processes governed by genetic drift, the small effects of such mutations make them difficult to study empirically. Here we present the results of a mutation-accumulation experiment designed to assess the frequencies of deleterious mutations with undetectable effects. We promoted the accumulation of spontaneous mutations by subjecting independent lineages of the RNA virus 6 to repeated population bottlenecks of a single individual. We measured fitness following every bottleneck to obtain a complete picture of the timing and effects of the accumulated mutations with detectable effects and sequenced complete genomes to determine the number of mutations that were undetected by the fitness assays. To estimate the effects of the undetected mutations, we implemented a likelihood model developed for quantitative trait locus (QTL) data (Otto and Jones 2000) to estimate the number and effects of the undetected mutations from the measured number and effects of the detected mutations. Using this method we estimated a deleterious mutation rate of U = 0.03 and a gamma effects distribution with mean s=0.093 and coefficient of variation = 0.204. Although our estimates of U and s fall within the range of recent mutation rate and effect estimates in eukaryotes, the fraction of mutations with detectable effects on laboratory fitness (39%) appears to be far higher in 6 than in eukaryotes.

Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination.

The nematode-borne Grapevine fanleaf virus, from the genus Nepovirus in the family Comoviridae, causes severe degeneration of grapevines in most vineyards worldwide. We characterized 347 isolates from transgenic and conventional grapevines from two vineyard sites in the Champagne region of France for their molecular variant composition. The population structure and genetic diversity were examined in the coat protein gene by IC-RT-PCR-RFLP analysis with EcoRI and StyI, and nucleotide sequencing, respectively. RFLP data suggested that 55 % (191 of 347) of the isolates had a population structure consisting of one predominant variant. Sequencing data of 51 isolates representing the different restrictotypes confirmed the existence of mixed infection with a frequency of 33 % (17 of 51) and showed two major predominant haplotypes representing 71 % (60 of 85) of the sequence variants. Comparative nucleotide diversity among population subsets implied a lack of genetic differentiation according to host (transgenic vs conventional) or field site for most restrictotypes (17 of 18 and 13 of 18) and for haplotypes in most phylogenetic groups (seven of eight and six of eight), respectively. Interestingly, five of the 85 haplotypes sequenced had an intermediate divergence (0.036-0.066) between the lower (0.005-0.028) and upper range (0.083-0.138) of nucleotide variability, suggesting the occurrence of homologous RNA recombination. Sequence alignments clearly indicated a mosaic structure for four of these five variants, for which recombination sites were identified and parental lineages proposed. This is the first in-depth characterization of the population structure and genetic diversity in a nepovirus.

Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products.

In order to investigate the genetic diversity of Potato leafroll virus (PLRV), seven new complete genomic sequences of isolates collected worldwide were compared with the five sequences available in GenBank. Then, a restricted polymorphic region of the genome was chosen to further analyse new sequences. The sequences of PLRV open reading frames (ORFs) 3 and 4 were also compared with those of two other poleroviruses and the non-synonymous to synonymous substitution ratio distribution was analysed in overlapping and non-overlapping regions of the genome using maximum-likelihood models. Results confirmed that PLRV sequences from around the world are very closely related and showed that the region encoding protein P0 allowed the detection of three groups of isolates. When compared to other poleroviruses, PLRV was the most conserved in both ORFs 3 and 4. However, the results suggest that important events, such as deletion, mutation at a stop codon and intraspecific homologous recombination events, have occurred during the evolution of PLRV. Finally, it was shown that the translation products of ORFs 0 and 3 are significantly more conserved than those of the overlapping ORFs 1 and 4, respectively. All together, the results allow the proposal of new hypotheses to explain the apparent genetic stability of PLRV and its evolution.