Genetic Differentiation and Migration Fluxes of Viruses from Melon Crops and Crop Edge Weeds.

Weeds surrounding crops may act as alternative hosts, playing important epidemiological roles as virus reservoirs and impacting virus evolution. We used high-throughput sequencing to identify viruses in Spanish melon crops and plants belonging to three pluriannual weed species, Ecballium elaterium, Malva sylvestris, and Solanum nigrum, sampled at the edges of the crops. Melon and E. elaterium, both belonging to the family Cucurbitaceae, shared three virus species, whereas there was no virus species overlap between melon and the other two weeds. The diversity of cucurbit aphid-borne yellows virus (CABYV) and tomato leaf curl New Delhi virus (ToLCNDV), both in melon and E. elaterium, was further studied by amplicon sequencing. Phylogenetic and population genetics analyses showed that the CABYV population was structured by the host, identifying three sites in the CABYV RNA-dependent RNA polymerase under positive selection, perhaps reflecting host adaptation. The ToLCNDV population was much less diverse than the CABYV one, likely as a consequence of the relatively recent introduction of ToLCNDV in Spain. In spite of its low diversity, we identified geographical but no host differentiation for ToLCNDV. Potential virus migration fluxes between E. elaterium and melon plants were also analyzed. For CABYV, no evidence of migration between the populations of the two hosts was found, whereas important fluxes were identified between geographically distant subpopulations for each host. For ToLCNDV, in contrast, evidence of migration from melon to E. elaterium was found, but not the other way around. IMPORTANCE It has been reported that about half of the emerging diseases affecting plants are caused by viruses. Alternative hosts often play critical roles in virus emergence as virus reservoirs, bridging host species that are otherwise unconnected and/or favoring virus diversification. In spite of this, the viromes of potential alternative hosts remain largely unexplored. In the case of crops, pluriannual weeds at the crop edges may play these roles. Here, we took advantage of the power of high-throughput sequencing to characterize the viromes of three weed species frequently found at the edges of melon crops. We identified three viruses shared by melon and the cucurbit weed, with two of them being epidemiologically relevant for melon crops. Further genetic analyses showed that these two viruses had contrasting patterns of diversification and migration, providing an interesting example on the role that weeds may play in the ecology and evolution of viruses affecting crops.

Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum.

Wild plants and weeds growing close to crops constitute a potential reservoir for future epidemies or for the emergence of novel viruses but the frequency and directionality of viral flow between cultivated and wild plants remains poorly documented in many cases. Here, we studied the diversity of viral populations between tomato (Solanum lycopersicum) and neighboring european black nightshade (Solanum nigrum) using high throughput sequencing (HTS) based metagenomics. A large variability in virome richness with only 17.9% shared Operational Taxonomy Units between tomato and nightshade, but this richness could not be linked to a particular host or to local conditions. A detailed population analysis based on assembled contigs for potato virus Y (PVY), broad wilt bean virus 1 and a new ilarvirus tentatively named Solanum nigrum ilarvirus 1 provides information on the circulation of these viruses between these two Solanum species and enriches our knowledge of the tomato virome.

The complete genome sequence of wild tomato mosaic virus isolated from Solanum nigrum reveals recombination in the P1 cistron.

The complete genome sequence of a wild tomato mosaic virus (WTMV) isolate (named WTMV-Sn) was determined and identified in Solanum nigrum in China. The complete genome of WTMV-Sn is 9,659 nucleotides in length, excluding the poly(A) tail and encodes a polyprotein of 3,074 amino acids. This is the first report of WTMV infecting S. nigrum. Despite the high degree of sequence similarity between the WTMV-Sn and WTMV-XC-1 isolates, the 349 nucleotides at the 5' terminus of WTMV-Sn appear to have originated by recombination with another isolate. The recombination parent remains unknown, but the recombination region shares 74.57% sequence identity with isolate WTMV-Laichau, which is below the species demarcation threshold for the genus Potyvirus. A pathogenicity test showed that WTMV-Sn can infect tobacco. This suggests that variation in the P1 cistron of WTMV-Sn may contribute to its ability to infect S. nigrum.

Organogénesis directa in vitro a partir de hojas de la planta antiplasmodial solanum nudum dunal / Direct organogenesis in vitro from leaves of solanum nudum dunal – antiplasmodial plant

Solanum nudum Dunal (Solanaceae), es una especie vegetal con potencial para desarrollar un tratamiento quimioterapéutico contra la malaria. Este es el primer reporte de un protocolo rápido, eficiente y reproducible de organogénesis directa a partir de segmentos de hoja de plántulas in vitro de esta especie.Los segmentos de hojas de plántulas de 5 meses de germinadas fueron cultivados sobre medio Murashige y Skoog (MS) a mitad de sales y vitaminas, con diferentes concentraciones de Bencilaminopurina (BAP), en combinación con Acido Indolacético (AIA). Se evaluó también el efecto de la iluminación en periodos 0/45, 15/30 y 30/15 días oscuridad/ luz, sobre la inducción de brotes. Se registró un promedio alto de formación de brotes (4,83) en explantes cultivados en medio suplementado con 2,0 mg/L de BAP y 0,1 mg/L de AIA, bajo condición de iluminación por un periodo de 30/15 días oscuridad/luz. Luego de la inducción, los brotes obtenidos fueron transferidos a medio MS suplementado con 0,3 mg/L de Giberelina (GA3), y mantenidos en condiciones de luz donde también enraizaron. Las plántulas regeneradas se llevaron a condiciones de invernadero y fueron morfológicamente similares a las plantas madres.

Solanum nudum Dunal (Solanaceae) is a plant with a potential for developing chemotherapeutic treatments against malaria. This is the first report of a fast, efficient, and reproducible direct organogenesis protocol from leave segments from in vitro seed-grown plantlets.Leaves segments from 5 months old germinated plantlets were placed on half concentration Murashige and Skoog medium (MS), supplemented with several concentrations of Bencilaminopurin (BAP) combinated with Indolacetic Acid (IAA). Dark/ light incubation effect in periods 0/45, 15/30 and 30/15 dark/light days were evaluated on the buds induction. High frequency buds formation was shown (4,83) in explants cultured on MS supplemented with BAP 2,0 mg/L and AIA 0,1 mg/L under a period of 30 days of dark condition incubation. After induction, buds obtained were transferred to MS medium supplemented with gibberellic acid (GA3) 0,3 mg/L and maintained under artificial cool light, there the plantlets rooted. Regenerated plantlets were placed under greenhouse conditions and these were morphologically similar to donor plants.

Begomovirus genetic diversity in the native plant reservoir Solanum nigrum: Evidence for the presence of a new virus species of recombinant nature.

We examined the native plant host Solanum nigrum as reservoir of genetic diversity of begomoviruses that cause the tomato yellow leaf curl disease (TYLCD) emerging in southern Spain. Presence of isolates of all the species and strains found associated with TYLCD in this area was demonstrated. Mixed infections were common, which is a prerequisite for recombination to occur. In fact, presence of a novel recombinant begomovirus was demonstrated. Analysis of an infectious clone showed that it resulted from a genetic exchange between isolates of the ES strain of Tomato yellow leaf curl Sardinia virus and of the type strain of Tomato yellow leaf curl virus. The novel biological properties suggested that it is a step forward in the ecological adaptation to the invaded area. This recombinant represents an isolate of a new begomovirus species for which the name Tomato yellow leaf curl Axarquia virus is proposed. Spread into commercial tomatoes is shown.