BUSCADOR RECOLECTA

Background: The known plant viruses mostly infect angiosperm hosts and have RNA or small DNA genomes. The only other lineage of green plants with a relatively well-studied virome, unicellular chlorophyte algae, is mostly infected by viruses with large DNA genomes. Thus RNA viruses and small DNA viruses seem to completely displace large DNA virus genomes in late branching angiosperms. To understand better the expansion of RNA viruses in the taxonomic span between algae and angiosperms, we analyzed the transcriptomes of 66 non-angiosperm plants characterized by the 1000 Plants Genomes Project.

Results: We found homologs of virus RNA-dependent RNA polymerases in 28 non-angiosperm plant species, including algae, mosses, liverworts (Marchantiophyta), hornworts (Anthocerotophyta), lycophytes, a horsetail Equisetum, and gymnosperms. Polymerase genes in algae were most closely related to homologs from double-stranded RNA viruses leading latent or persistent lifestyles. Land plants, in addition, contained polymerases close to the homologs from single-stranded RNA viruses of angiosperms, capable of productive infection and systemic spread. For several polymerases, a cognate capsid protein was found in the same library. Another virus hallmark gene family, encoding the 30 K movement proteins, was found in lycophytes and monilophytes but not in mosses or algae.

Conclusions: The broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction., We thank the colleagues at the 1000 Plant Genomes Project for helping us to access the transcriptomes used in this study via the iPlant Collaborative. We are grateful to Javier Forment (IBMCP-CSIC), Vincent Lefort (PhyML), and the E-Biothon team (E-Biothon platform is supported by CNRS, IBM, INRIA, l'Institut Francais de Bioinformatique and SysFera) for expert help with high-performance computing; to Yuri Wolf, Jan Kreuze, Eddie Holmes, and Mang Shi for sharing sequence data and alignments; to Sejo Sabanadzovic, Jan Kreuze, and the anonymous reviewers for helpful virtual discussions and critical remarks; and to Natalia Mushegian for technical assistance. SFF was supported by grants BFU2015-65037P from Spain Ministry of Economy and Competitiveness and PROMETEOII/2014/021 from Generalitat Valenciana. ARM is a Program Director at the US National Science Foundation (NSF); his work on this project was supported by the NSF Independent Research and Development Program, but the statements and opinions expressed herein are made in the personal capacity and do not constitute the endorsement by NSF or the government of the United States.

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically
redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viralfitness. Moreover,uponanalyzing thegenomesof theevolved viruses,wealways observedthedeletionof
the duplicated gene copy andmaintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data,wedeveloped a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability.Acontext-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes., We thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance. This work was supported by the John Templeton Foundation [grant number 22371 to S.F.E.]; the European Commission 7th Framework Program EvoEvo Project [grant number ICT-610427 to S.F.E.]; the Spanish Ministerio de Economia y Competitividad (MINECO) [grant numbers BFU2012-30805 and BFU2015-65037-P to S.F.E.]; the Botin Foundation from Banco Santander through its Santander Universities Global Division [J.S.]; the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya [J.S.]; and the European Molecular Biology Organization [grant number ASTF 625-2015 to A.W]. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

[EN] Adaptive fitness landscapes are a fundamental concept in evolutionary biology that relate the genotype of individuals with their fitness. At the end, the evolutionary fate of evolving populations depends on the topography of the landscape, that is, the number of accessible mutational pathways and of possible fitness peaks (i.e, adaptive solutions). For long time, fitness landscapes were only theoretical constructions due to a lack of precise information on the mapping between genotypes and phenotypes. In recent years, however, efforts have been devoted to characterize the properties of empirical fitness landscapes for individual proteins or for microbes adapting to artificial environments. In a previous study, we had characterized the properties of the empirical fitness landscape defined by the first five mutations fixed during adaptation of tobacco etch potyvirus (TEV) to a new experimental host, Arabidopsis thaliana. Here we evaluate the topography of this landscape in the ancestral host Nicotiana tabacum. Comparing the topographies of the landscape in the two hosts, we found that some features remain similar, such as the existence of fitness holes and the prevalence of epistasis, including cases of sign and of reciprocal sign that create rugged, uncorrelated and highly random topographies. However, we also observed significant differences in the fine grained details among both landscapes due to changes in the fitness and epistatic interactions of some genotypes. Our results support the idea that not only fitness tradeoffs between hosts but also topographical incongruences among fitness
landscapes in alternative hosts may contribute to virus specialization., This project was funded by grants BFU2012-30805 and BFU2015-65037P from the Spanish Ministry of Economy and Competitiveness (MINECO), PROMETEOII/2014/021 from the Generalitat Valenciana, and EvoEvo (ICT610427) from the European Commission 7th Framework Program to S.F.E. H.C. was supported by contract BES2013-065595 from MINECO. J.L. was supported by a JAE-pre contract from CSIC.

[EN] Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it., This project was funded by grant nos. BFU2012-30805 and BFU2015-65037P from the Spanish Ministry of Economy and Competitiveness (MINECO), PROMETEOII/2014/021 from Generalitat Valenciana and EvoEvo (ICT610427) from the European Commission 7th Framework Program to S.F.E. H.C. was supported by contract BES2013-065595 from MINECO. J.L. was supported by a JAE-pre contract from CSIC.

[EN] Background: Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations. Thereby, this alternative explanation limits the microparasites' potential to adapt to the host and ultimately the ability to evolve lower virulence. As a first exploration of this hypothesis, we evolved Tobacco etch virus carrying an eGFP fluorescent marker in two semi-permissive host species, Nicotiana benthamiana and Datura stramonium, for which it has a large difference in virulence. We compared the results to those previously obtained in the natural host, Nicotiana tabacum, where we have shown that carriage of eGFP has a high fitness cost and its loss serves as a real-time indicator of adaptation.

Results: After over half a year of evolution, we sequenced the genomes of the evolved lineages and measured their fitness. During the evolution experiment, marker loss leading to viable virus variants was only observed in one lineage of the host for which the virus has low virulence, D. stramonium. This result was consistent with the observation that there was a fitness cost of eGFP in this host, while surprisingly no fitness cost was observed in the host for which the virus has high virulence, N. benthamiana. Furthermore, in both hosts we observed increases in viral fitness in few lineages, and host-specific convergent evolution at the genomic level was only found in N. benthamiana.

Conclusions: The results of this study do not lend support to the hypothesis that high virulence impedes microparasites' evolution. Rather, they exemplify that jumps between host species can be game changers for evolutionary dynamics. When considering the evolution of genome architecture, host species jumps might play a very important role, by allowing evolutionary intermediates to be competitive., This work was supported by the John Templeton Foundation [grant number 22371 to S.F.E]; the European Commission 7th Framework Program EvoEvo Project [grant number ICT-610427 to S.F.E.]; and the Spanish Ministerio de Economia y Competitividad (MINECO) [grant numbers BFU2012-30805 and BFU2015-65037-P to S.F.E]. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

[EN] Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide.
Understanding the factors that influence its evolutionary success is essential for developing new control strategies that
may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of
mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on
a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced
nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also
explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic
interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced
in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured., This study was financially supported by grant 2011/01/D/NZ9/00279, from the Poland National Science Center, to B.H.J and by grants BFU2015-65037-P, from Spain Ministry of Economy and Competitiveness-FEDER, and PROMETEOII/2014/021, from Generalitat Valenciana, to S.F.E.

[EN]

Understanding how genetic drift, mutation and selection interplay in determining the evolutionary fate of populations is one of the central themes of Evolutionary Biology. Theory predicts that by increasing the number of coexisting beneficial alleles in a population beyond some point does not necessarily translates into an acceleration in the rate of evolution. This diminishing-returns effect of beneficial genetic variability in microbial asexual populations is known as clonal interference. Clonal interference has been shown to operate in experimental populations of animal RNA viruses replicating in cell cultures. Here we carried out experiments to test whether a similar diminishing-returns of population size on the rate of adaptation exists for a plant RNA virus infecting real multicellular hosts. We have performed evolution experiments with tobacco etch potyvirus in two hosts, the natural and a novel one, at different inoculation sizes and estimated the rates of evolution for two phenotypic fitness-related traits. Firstly, we found that evolution proceeds faster in the novel than in the original host. Secondly, results were compatible with a diminishing-returns effect of inoculum size on the rate of evolution for one of the fitness traits, but not for the other, which suggests that selection operates differently on each trait., We thank F. DE LA IGLESIA and P. AGUDO for excellent technical support and J. A. CUESTA for critical reading and insightful suggestions. This work was supported by grant BFU2015-65037-P from Spain's Ministry of Economy, Industry and Competitiveness and by the Santa Fe Institute.

[EN] Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified and sequenced its full-length genomic RNA which identified the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we investigated the host range of the Spanish ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV. This is the first observation of ToMMV in tomato plants in Europe. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods., This work was supported by grants BFU2015-70261-P and BFU2015-65037-P (to C.H. and S.F.E., respectively) from Spain Ministry of Economy, Industry and Competitiveness/FEDER.

[EN] The existence of multipartite viruses is an intriguing mystery in evolutionary virology. Several hypotheses suggest benefits that should outweigh the costs of a reduced transmission efficiency and of segregation of coadapted genes associated with encapsidating each segment into a different particle. Advantages range from increasing genome size despite high mutation rates, faster replication, more efficient selection resulting from reassortment during mixed infections, better regulation of gene expression, or enhanced virion stability and cell-to-cell movement. However, support for these hypotheses is scarce. Here we report experiments testing whether an evolutionary stable equilibrium exists for the three genomic RNAs of Alfalfa mosaic virus (AMV). Starting infections with different segment combinations, we found that the relative abundance of each segment evolves towards a constant ratio. Population genetic analyses show that the segment ratio at this equilibrium is determined by frequency-dependent selection. Replication of RNAs 1 and 2 was coupled and collaborative, whereas the replication of RNA 3 interfered with the replication of the other two. We found that the equilibrium solution is slightly different for the total amounts of RNA produced and encapsidated, suggesting that competition exists between all RNAs during encapsidation. Finally, we found that the observed equilibrium appears to be host-species dependent., We thank Francisca de la Iglesia, Paula Agudo and Lorena Corachan for their dedication and expert technical assistance. This project was funded in part by grants BFU2015-65037P from the Spanish Ministry of Economy and Competitiveness-FEDER, PROMETEOII/2014/021 from Generalitat Valenciana and EvoEvo (ICT610427) from the European Commission 7th Framework Program to S.F.E. The China Scholarship Council and the Chinese Academy of Agricultural Sciences provided funding to B.W.

[EN] Horizontal gene transfer (HGT) is pervasive in viruses and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here, we explore experimentally the evolutionary fate of viruses with simulated HGT events, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome. One of the events simulates the acquisition of a new function though HGT of a conserved AlkB domain, responsible for the repair of alkylation or methylation damage in many organisms. The other event simulates the acquisition of a sequence that duplicates an existing function, through HGT of the 2b RNA silencing suppressor from Cucumber mosaic virus. We then evolved these two viruses, tracked the maintenance of the horizontally transferred sequences over time, and for the final virus populations, sequenced their genome and measured viral fitness. We found that the AlkB domain was rapidly purged from the TEV genome, restoring fitness to wild-type levels. Conversely, the 2b gene was stably maintained and did not have a major impact on viral fitness. Moreover, we found that 2b is functional in TEV, as it provides a replicative advantage when the RNA silencing suppression domain of HC-Pro is mutated. These observations suggest a potentially interesting role for HGT of short functional sequences in ameliorating evolutionary constraints on viruses, through the duplication of functions., We thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance. This work was supported by the John Templeton Foundation (grant 22371), the European Commission 7th Framework Program EvoEvo Project (grant ICT-610427), and the Spanish Ministerio de Economia y Competitividad (grants BFU2012-30805 and BFU2015-65037-P) to S.F.E. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

[EN] For multihost pathogens, adaptation to multiple hosts has important implications for
both applied and basic research. At the applied level, it is one of the main factors
determining the probability and severity of emerging disease outbreaks. At the basic
level, it is thought to be a key mechanism for the maintenance of genetic diversity
both in host and pathogen species. In recent years, a number of evolution experiments
have assessed the fate of plant virus populations replicating within and adapting to
one single or to multiple hosts species. A first group of these experiments tackled the
existence of trade-offs in fitness and virulence for viruses evolving either within a single
hosts species or alternating between two different host species. A second set of
experiments explored the role of genetic variability in susceptibility and resistance to
infection among individuals from the same host species in the extent of virus local
adaptation and of virulence. In general, when a single host species or genotype is
available, these experiments show that local adaptation takes place, often but not
always associated with a fitness trade-off. However, alternating between different host
species or infecting resistant host genotypes may select for generalist viruses that experience
no fitness cost. Therefore, the expected cost of generalism, arising from antagonistic
pleiotropy and other genetic mechanisms generating fitness trade-offs between
hosts, could not be generalized and strongly depend on the characteristics of each particular
pathosystem. At the genomic level, these studies show pervasive convergent
molecular evolution, suggesting that the number of accessible molecular pathways
leading to adaptation to novel hosts is limited., I thank all my past and present collaborators engaged in the endeavour of understanding the mechanisms and processes driving RNA viruses adaptation to their reservoir and new hosts. I also thank Britt Koskella, Anna-Liisa Laine and Tatiana Giraud for inviting me to contribute to this special issue. The constructive comments and suggestions from one reviewer are greatly appreciated. Nowadays, my research is supported by grants BFU2015-65037-P (Spanish Ministry of Economy and Competitiveness), PROMETEOII/2014/021 (Generalitat Valenciana) and the ICT610427 EvoEvo project (European Commission 7th Framework Program).

[EN] Functional redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is considered as a source of genetic and functional innovation. In any case, genetically redundant genes are expected to show an acceleration in the rate of molecular evolution. Here, we tackle the role of functional redundancy in viral RNA genomes. To this end, we have evaluated the rates of compensatory evolution for deleterious mutations affecting an essential function, the suppression of RNA silencing plant defense, of tobacco etch potyvirus (TEV). TEV genotypes containing deleterious mutations in presence/absence of engineered functional redundancy were evolved and the pattern of fitness and pathogenicity recovery evaluated. Genetically redundant genotypes suffered less from the effect of deleterious mutations and showed relatively minor changes in fitness and pathogenicity. By contrast, nongenetically redundant genotypes had very low fitness and pathogenicity at the beginning of the evolution experiment that were fully recovered by the end. At the molecular level, the outcome depended on the combination of the actual mutations being compensated and the presence/absence of functional redundancy. Reversions to wild-type alleles were the norm in the nonredundant genotypes while redundant ones either did not fix any mutation at all or showed a higher nonsynonymous mutational load., We thank Paula Agudo for excellent technical assistance. This work was supported by Spain's Agencia Estatal de Investigacion-FEDER grant BFU2015-65037-P to S.F.E. and by a fellowship from the Dominican Republic's Ministerio de Educacion Superior, Ciencia y Tecnologia to S.M.R. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the article.

[EN] Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness., This work was supported by the John Templeton Foundation (grant 22371), the European Commission seventh Framework Program EvoEvo Project (grant ICT-610427), and Spain Agencia Estatal de Investigacion-FEDER (grant BFU2015-65037-P) to S.F.E. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.

[EN] Viral infections are extremely complex processes that could only be well understood by precisely characterizing the interaction networks between the virus and the host components. In recent years, much effort has gone in this directionwith the aimof unveiling themolecular basis of viral pathology. These networks are mostly formed by viral and host proteins, and are expected to be dynamic bothwith time and space (i.e., with the progression of infection, as well as with the virus and host genotypes; what we call plastodynamic). This largely overlooked spatio-temporal evolution urgently calls for a change both in the conceptual paradigms and experimental techniques used so far to characterize virus-host interactions. More generally, molecular plasticity and temporal dynamics
are unavoidable components of themechanisms that underlie any complex disease; components whose understandingwill eventually enhance our ability to modulate those networkswith the aimof improving disease treatments., This work is supported by the grants BFU2015-66894-P (to G.R.), BI02014-54269-R (to J-A.D.) and BFU2015-65037-P (to S.F.E.) from the Ministerio de Economia, Industria y Competitividad, and by the grant PROMETEOII/2014/021 from the Generalitat Valenciana (to S.F.E. and J-A.D.).

[EN] Tomato black ring virus (TBRV) is the only member of the Nepovirus genus that is known to form defective RNA particles (D RNAs) during replication. Here, de novo generation of D RNAs was observed during prolonged passages of TBRV isolates originated from Solanum lycopersicum and Lactuca sativa in Chenopodium quinoa plants. D RNAs of about 500 nt derived by a single deletion in the RNA1 molecule and contained a portion of the 5' untranslated region and viral replicase, and almost the entire 3' non coding region. Short regions of sequence complementarity were found at the 5' and 3' junction borders, which can facilitate formation of the D RNAs. Moreover, in this study we analyzed the effects of D RNAs on TBRV replication and symptoms development of infected plants. C. quinoa, S. lycopersicum, Nicotiana tabacum, and L. sativa were infected with the original TBRV isolates (TBRV-D RNA) and those containing additional D RNA particles (TBRV + D RNA). The viral accumulation in particular hosts was measured up to 28 days post inoculation by RT-qPCR. Statistical analyses revealed that D RNAs interfere with TBRV replication and thus should be referred to as defective interfering particles. The magnitude of the interference effect depends on the interplay between TBRV isolate and host species., This work was supported by the National Science Centre, Poland (grant number 2017/25/B/NZ9/01715); Ministry of Science and Higher Education, Poland (grant number IP2014 014973) (to B.H.-J.) and Spain Agencia Estatal de Investigacion-FEDER (grant number BFU2015-65037P) (to S.F.E.). The funding bodies were not involved into the design of the study, analysis, and interpretation of data in the manuscript.

[EN] Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts., We thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance, the EvolSysVir lab members for help, comments and discussions, Rachel Whitaker for English proofreading, and Lorena Latorre (IBMCP Genomics Service) and Javier Forment (IBMCP Bioinformatics Service) for their assistance. This research was supported by grants from Spain's Agencia Estatal de Investigacion-FEDER (BFU2012-30805 and BFU2015-65037-P to S.F.E. and BFU2015-66894-P to G.R.) and Generalitat Valenciana (PROMETEOII/2014/021).

[EN] Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called 'stamping machine replication' (SMR) and 'geometric replication' (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasi-neutral coexistence scenario, with a line of fixed points involving different strands' equilibrium ratios depending on the initial conditions. Recent research into the quasi-neutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alter the mean-field scenario, and one of the two species outcompetes the other. In this article, we study this phenomenon for viral RNA replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNAs, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication., The research leading to these results has received funding from 'la Caixa' Foundation. J.S. and T.A. have been partially funded by the CERCA Program of the Generalitat de Catalunya, MINECO grant no. MTM2015-71509-C2-1-R and by a MINECO grant awarded to the Barcelona Graduate School of Mathematics under the 'Maria de Maeztu' Program (grant no. MDM-2014-0445). T.A. is also supported by AGAUR (grant no. 2014SGR1307). S.F.E. has been supported by MINECO-FEDER grant no. BFU2015-65037-P and by Generalitat Valenciana grant no. PROMETEOII/2014/021.

[EN] RNA viruses are one of the fastest evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly-generated variation in the evolving viral lineages. A time-sampled approach allowed us to: (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less susceptible host (efficient in the accumulation of salicylicacid)., This study was supported by the Slovenian Research Agency (grants L4-5525 and P4-0165 and Ph.D. grant to D.K.). Work in Valencia was supported by Spain Ministry of Economy and Competitiveness (grant BFU2015-65037-P to S.F.E.), and short-term scientific mission support was provided to D.K. in the frame of EU-funded COST action FA1407.

[EN] Ecological networks, both displaying mutualistic or antagonistic interactions, seem to share common structural traits: the presence of nestedness and modularity. A variety of model approaches and hypothesis have been formulated concerning the significance and implications of these properties. In phage-bacteria bipartite infection networks, nestedness seems to be the rule in many different contexts. Modeling the coevolution of a diverse virus¿host ensemble is a difficult task, given the dimensionality and multi parametric nature of a standard continuous approximation. Here, we take a different approach, by using a neutral, toy model of host¿phage interactions on a spatial lattice. Each individual is represented by a bit string (a digital genome) but all strings in each class (i.e. hosts or phages) share the same sets of parameters. A matching allele model of phage-virus recognition rule is enough to generate a complex, diverse ecosystem with heterogeneous patterns of interaction and nestedness, provided that interactions take place under a spatially constrained setting. It is found that nestedness seems to be an emergent property of the co-evolutionary dynamics. Our results indicate that the enhanced diversity resulting from localized interactions strongly promotes the presence of nested infection matrices., The authors would like to thank the members of the Complex Systems Lab and our colleagues at the Santa Fe Institute for fruitful discussions. This work has been supported by the Botin Foundation by Banco Santander through its Santander Universities Global Division. This work was supported by the grants BFU2015-65037-P (S.F.E.) and FIS2016-77447-R (S.V.) from Spain Ministerio de Economia, Industria y Competitividad, AEI/MINEICO/FEDER and UE. The authors also thank the Santa Fe Institute, wheremost of this work was done

[EN] The existence of cooperation, or the production of public goods, is an evolutionary
problem. Cooperation is not favoured because the Prisoner s
Dilemma (PD) game drives cooperators to extinction. We have re-analysed
this problem by using RNA viruses to motivate a model for the evolution of
cooperation. Gene products are the public goods and group size is the
number of virions co-infecting the same host cell. Our results show that if
the trade-off between replication and production of gene products is linear,
PD is observed. However, if the trade-off is nonlinear, the viruses evolve
into separate lineages of ultra-defectors and ultra-cooperators as group size
is increased. The nonlinearity was justified by the existence of real viral
ultra-defectors, known as defective interfering particles, which gain a nonlinear
advantage by being smaller. The evolution of ultra-defectors and
ultra-cooperators creates the Snowdrift game, which promotes high-level
production of public goods., Work was supported by grants to L.C. from the National Science Foundation (DEB-1354253) and to S.F.E. from Spain's Ministries of Education, Culture and Sport (Salvador de Madariaga Programme PRX15/00149) and Economy, Industry and Competitiveness (BFU2015-65037-P), Generalitat Valenciana (PROMETEOII/2014/021) and the European Commission 7th Framework Programme EvoEvo Project (grant ICT-610427)

[EN] Predicting viral emergence is difficult due to the stochastic nature of the underlying processes and the many factors that govern pathogen evolution. Environmental factors affecting the host, the pathogen and the interaction between both are key in emergence. In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in their environments. A broad knowledge of these factors will allow better estimating where and when viral emergence is more likely to occur. Here, we investigate how the population structure for susceptibility-to-infection genes of the plant Arabidopsis thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have evolved TuMV lineages in two radically different host population structures: (1) a metapopulation subdivided into six demes (subpopulations); each one being composed of individuals from only one of six possible A. thaliana ecotypes and (2) a well-mixed population constituted by equal number of plants from the same six A. thaliana ecotypes. These two populations were evolved for twelve serial passages. At the end of the experimental evolution, we found faster adaptation of TuMV to each ecotype in the metapopulation than in the well-mixed heterogeneous host populations. However, viruses evolved in well-mixed populations were more pathogenic and infectious than viruses evolved in the metapopulation. Furthermore, the viruses evolved in the demes showed stronger signatures of local specialization than viruses evolved in the well-mixed populations. These results illustrate how the genetic diversity of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen., We thank Francisca de la Iglesia for continuous excellent technical support. Work was supported by Spain's Agencia Estatal de Investigacion-FEDER grant BFU2015-65037-P and Generalitat Valenciana grant GRISOLIA/2018/005 to S.F.E. R.G. was supported by Spain's Agencia Estatal de Investigacion pre-doctoral contract BES-2016-077078.

[EN] Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations., This work was funded by Spain's Agencia Estatal de Investigacion-FEDER grant BFU201565037-P and Generalitat Valenciana grant PROMETEU2019/012 to S.F.E. R.G. and A.B. were supported by Ministerio de Ciencia, Innovacion y Universidades-FEDER contract BES-2016-077078 and Generalitat Valenciana grant GRISOLIAP/2018/005, respectively.

[Background]: The known plant viruses mostly infect angiosperm hosts and have RNA or small DNA genomes. The only other lineage of green plants with a relatively well-studied virome, unicellular chlorophyte algae, is mostly infected by viruses with large DNA genomes. Thus RNA viruses and small DNA viruses seem to completely displace large DNA virus genomes in late branching angiosperms. To understand better the expansion of RNA viruses in the taxonomic span between algae and angiosperms, we analyzed the transcriptomes of 66 non-angiosperm plants characterized by the 1000 Plants Genomes Project. [Results]:
We found homologs of virus RNA-dependent RNA polymerases in 28 non-angiosperm plant species, including algae, mosses, liverworts (Marchantiophyta), hornworts (Anthocerotophyta), lycophytes, a horsetail Equisetum, and gymnosperms. Polymerase genes in algae were most closely related to homologs from double-stranded RNA viruses leading latent or persistent lifestyles. Land plants, in addition, contained polymerases close to the homologs from single-stranded RNA viruses of angiosperms, capable of productive infection and systemic spread. For several polymerases, a cognate capsid protein was found in the same library. Another virus hallmark gene family, encoding the 30 K movement proteins, was found in lycophytes and monilophytes but not in mosses or algae. [Conclusions]: The broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for
Research (URICI)., SFE was supported by grants BFU2015-65037P from Spain Ministry of Economy and Competitiveness and PROMETEOII/2014/021 from Generalitat Valenciana. ARM is a Program Director at the US National Science Foundation (NSF); this work on this project was supported by the NSF Independent Research and Development Program., Peer reviewed

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes., This work was supported by the John Templeton Foundation [grant number 22371 to S.F.E.]; the European Commission 7th Framework Program EvoEvo Project [grant number ICT-610427 to S.F.E.]; the Spanish Ministerio de Economía y Competitividad (MINECO) [grant numbers BFU2012-30805 and BFU2015-65037-P to S.F.E.]; the Botín Foundation from Banco Santander through its Santander Universities Global Division [J.S.]; the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya [J.S.]; and the European Molecular Biology Organization [grant number ASTF 625-2015 to A.W]., Peer reviewed

Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date., P.C. is supported by a Ramón Areces Foundation Postdoctoral Fellowship. The Spanish Ministerio de Ciencia,
Innovación y Universidades-FEDER funds of the European Union support Projects BASIC (PGC2018-098186-B-I00,
J.A.C. and P.C.),MiMevo (FIS2017-89773-P, S.M.), and EvolSysVir (BFU2015-65037-P, S.F.E.).

[Background]: Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured., [Results]: A collection of 25 PepMV clones each containing a single nucleotide nonsynonymous substitution was created by site-directed mutagenesis and the fitness of each mutant was determined. PepMV-P22 genome showed a high degree of robustness against point mutations, with 80% of mutations being either neutral or even beneficial and only 20% being deleterious or lethal. We found that the effect of mutations strongly depended on the gene in which they were introduced. Mutations with the largest average beneficial effects were those affecting the RdRp gene, in contrast to mutations affecting TGB1 and CP genes, for which the average effects were deleterious. Moreover, significant epistatic interactions were observed between nonsynonymous mutations and the genetic background, meaning that the effect of a given nucleotide substitution on a particular genomic context cannot be predicted by knowing its effect in a different one., [Conclusions]: Our results indicated that PepMV genome has a surprisingly high robustness against mutations. We also found that fitness consequences of a given mutation differ between the two strains analyzed. This discovery suggests that the strength of selection, and thus the rates of evolution, vary among PepMV strains., This study was financially supported by grant 2011/01/D/NZ9/00279, from the Poland National Science Center, to B.H.J and by grants BFU2015-65037-P, from Spain Ministry of Economy and Competitiveness-FEDER, and PROMETEOII/2014/021, from Generalitat Valenciana, to S.F.E., Peer reviewed

Functional redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is considered as a source of genetic and functional innovation. In any case, genetically redundant genes are expected to show an acceleration in the rate of molecular evolution. Here, we tackle the role of functional redundancy in viral RNA genomes. To this end, we have evaluated the rates of compensatory evolution for deleterious mutations affecting an essential function, the suppression of RNA silencing plant defense, of tobacco etch potyvirus (TEV). TEV genotypes containing deleterious mutations in presence/absence of engineered functional redundancy were evolved and the pattern of fitness and pathogenicity recovery evaluated. Genetically redundant genotypes suffered less from the effect of deleterious mutations and showed relatively minor changes in fitness and pathogenicity. By contrast, nongenetically redundant genotypes had very low fitness and pathogenicity at the beginning of the evolution experiment that were fully recovered by the end. At the molecular level, the outcome depended on the combination of the actual mutations being compensated and the presence/absence of functional redundancy. Reversions to wild-type alleles were the norm in the nonredundant genotypes while redundant ones either did not fix any mutation at all or showed a higher nonsynonymous mutational load., This work was supported by Spain’s Agencia Estatal de Investigacion—FEDER grant BFU2015-65037-P to S.F.E. and by a fellowship from the Dominican Republic’s Ministerio de
Educacion Superior, Ciencia y Tecnolog ıa to S.M.R., Peer reviewed

Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate—the rate at which deletions removing the insertion occur—and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness., This work was supported by the John Templeton Foundation (grant 22371), the European Commission seventh Framework Program EvoEvo Project (grant ICT-610427), and Spain Agencia Estatal de Investigación-FEDER (grant BFU2015-65037-P) to S.F.E., Peer reviewed

Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts., This research was supported by grants from Spain’s Agencia Estatal de Investigacion—FEDER
(BFU2012-30805 and BFU2015-65037-P to S.F.E. and BFU2015-66894-P to G.R.) and Generalitat Valenciana (PROMETEOII/2014/021)., Peer reviewed

A new mycovirus was identified in Trichoderma harzianum strain 137 isolated in Xinjiang province, China. The whole genome sequence of the mycovirus was determined by metagenomic sequencing, RT-PCR, and RACE cloning. The mycovirus contained two genomic segments. The first segment was 2088 bp long and contained a single ORF (ORF1) encoding the RNA-dependent RNA polymerase (RdRP) (72.26 kDa). The second segment was 1634 bp long and also contained a single ORF (ORF2) encoding a hypothetical protein of 37.472 kDa. We named this novel mycovirus "Trichoderma harzianum bipartite mycovirus 1" (ThBMV1). Phylogenetic analysis showed that ThBMV1 clusters with other unclassified dsRNA mycoviruses., This work was supported by the National Key Research and Development Plan (Chemical fertilizer and pesticide reducing efficiency synergistic technology research and development): Research and demonstration of a new high efficiency biocide (2017YFD0201100-2017YFD0201102) granted to Xiliang Jiang; Research and demonstration of technology integration on reducing chemical fertilizer and pesticide application in open field vegetables (2018YFD0201200-2018YFD0201202) granted to Mei Li; Demonstration of comprehensive prevention and control technology of non-point source pollution in main vegetable producing areas of Huang Huai Hai (SQ2018YFD080026) granted to Beilei Wu; Work in València was supported by Spain’s Agencia Estatal de Investigación - FEDER grant BFU2015-65037-P granted to Santiago F. Elena., Peer reviewed

RNA virus high mutation rate is a double-edged sword. At the one side, most mutations jeopardize proteins functions; at the other side, mutations are needed to fuel adaptation. The relevant question then is the ratio between beneficial and deleterious mutations. To evaluate this ratio, we created a mutant library of the 6K2 gene of tobacco etch potyvirus that contains every possible single-nucleotide substitution. 6K2 protein anchors the virus replication complex to the network of endoplasmic reticulum membranes. The library was inoculated into the natural host Nicotiana tabacum, allowing competition among all these mutants and selection of those that are potentially viable. We identified 11 nonsynonymous mutations that remain in the viral population at measurable frequencies and evaluated their fitness. Some had fitness values higher than the wild-type and some were deleterious. The effect of these mutations in the structure, transmembrane properties, and function of 6K2 was evaluated in silico. In parallel, the effect of these mutations in infectivity, virus accumulation, symptoms development, and subcellular localization was evaluated in the natural host. The α-helix H1 in the N-terminal part of 6K2 turned out to be under purifying selection, while most observed mutations affect the link between transmembrane α-helices H2 and H3, fusing them into a longer helix and increasing its rigidity. In general, these changes are associated with higher within-host fitness and development of milder or no symptoms. This finding suggests that in nature selection upon 6K2 may result from a tradeoff between within-host accumulation and severity of symptoms., Work in Valencia was supported by the Spanish Agencia Estatal de Investigacion - FEDER grant BFU2015-65037-P and Generalitat Valenciana’s grant PROMETEOII/2014/021 to S.F.E. Work in
Barcelona was supported by a European Research Council Consolidator grant (616434), the Spanish Ministry of Economy and Competitiveness (grants BFU2011-2606 and SEV-2012-0208), the AXA Research Fund, the Bettencourt Schueller Foundation, Agencia de Gestio d’Ajuts Universitaris i Recerca (SGR-831), the CRG Systems Biology Program, and the CERCA Program (Generalitat de Catalunya). B.W. was supported by the China Scholarship Council and the Chinese Academy of Agricultural Sciences. X.L. was supported by Fundacion Ramon Areces and CRG fellowships, Peer reviewed

Compared to the replication of double-stranded RNA and DNA viruses, the replication of single-stranded viruses requires the production of a number of intermediate strands that serve as templates for the synthesis of genomic-sense strands. Two theoretical extreme mechanisms for replication for such single-stranded viruses have been proposed; one extreme being represented by the so-called linear stamping machine and the opposite extreme by the exponential growth. Of course, real systems are more complex and examples have been described in which a combination of such extreme mechanisms can also occur: a fraction of the produced progeny resulting from a stamping-machine type of replication that uses the parental genome as template, whereas other fraction of the progeny results from the replication of other progeny genomes. Martínez et al., Sardanyés et al. and Fornés et al. suggested and analyzed a deterministic model of single-stranded RNA (ssRNA) virus intracellular replication that incorporated variability in the replication mechanisms. To explore how stochasticity can affect this mixed-model principal properties, in this paper, we consider the stability of a stochastically perturbed model of ssRNA virus replication within a cell. Using the direct Lyapunov method, we found sufficient conditions for the stability in probability of equilibrium states for this model. This result confirms that this heterogeneous model of single-stranded RNA virus replication is stable with respect to stochastic perturbations of the environment., Leonid Shaikhet is supported by the Israel Science Foundation via grant No. 1128/14 and the Israeli Ministry of Absorption. Santiago F. Elena is supported by Spain's Ministerio de Economía,
Industria y Competitividad grant BFU2015-65037-P and by Generalitat Valenciana grant PROMETEOII/2014/021. Andrei Korobeinikov is supported by the Spain's Ministerio de Economía,
Industria y Competitividad grant MTM2015-71509-C2-1-R., Peer reviewed

Efficient dispersion of Tomato torrado virus (ToTV), an emerging virus affecting tomato crops worldwide, is linked to its principal vectors, Bemisia tabaci and Trialeurodes vaporariorum. To evaluate whether ToTV can be seed-transmitted, we collected seeds from tomato varieties Beta Lux, Grace and Money Maker that had been mechanically inoculated with two ToTV isolates; seedlings were grown in an insect-proof glasshouse, then tested for ToTV by immunocapture-qRT-PCR. Among 17,985 plants, 69 were ToTV-positive (0.38% overall vertical transmission). Bioassays using indicator plants confirmed the presence of infectious virus in the seedlings. This is the first report of tomato seed transmission of ToTV., This study was supported by project N N310 732040 from National Science Centre of Poland. Work in Valencia was supported by grant BFU2015-65037-P from Spain’s Agencia Estatal de Investigación – FEDER., Peer reviewed

Tomato black ring virus (TBRV) is the only member of the Nepovirus genus that is known to form defective RNA particles (D RNAs) during replication. Here, de novo generation of D RNAs was observed during prolonged passages of TBRV isolates originated from Solanum lycopersicum and Lactuca sativa in Chenopodium quinoa plants. D RNAs of about 500 nt derived by a single deletion in the RNA1 molecule and contained a portion of the 5' untranslated region and viral replicase, and almost the entire 3' non-coding region. Short regions of sequence complementarity were found at the 5' and 3' junction borders, which can facilitate formation of the D RNAs. Moreover, in this study we analyzed the effects of D RNAs on TBRV replication and symptoms development of infected plants. C. quinoa, S. lycopersicum, Nicotiana tabacum, and L. sativa were infected with the original TBRV isolates (TBRV-D RNA) and those containing additional D RNA particles (TBRV + D RNA). The viral accumulation in particular hosts was measured up to 28 days post inoculation by RT-qPCR. Statistical analyses revealed that D RNAs interfere with TBRV replication and thus should be referred to as defective interfering particles. The magnitude of the interference effect depends on the interplay between TBRV isolate and host species., This work was supported by the National Science Centre, Poland (grant number 2017/25/B/NZ9/01715); Ministry of Science and Higher Education, Poland (grant number IP2014 014973) (to B.H.-J.) and Spain Agencia Estatal de Investigación-FEDER (grant number BFU2015-65037P) (to S.F.E.)., Peer reviewed

The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics., P.L. was supported by the European Union: European Regional Development Fund (ERDF), by the Conseil Régional de La Réunion and by the Centre de Coopération internationale en Recherche agronomique pour le Développement (CIRAD). S.F.E. was supported by a grant (BFU2015-65037-P) from Spain Ministry of Science, Innovation and Universities–ERDF., Peer reviewed

In this study, 267 coat protein gene (CP) sequences from 48 Polish isolates of Apple stem pitting virus (ASPV) were determined. The genetic structure of the virus population was analysed and possible mechanisms of molecular evolution explored. We found evidence of recombination within the ASPV population and the presence of 17 ASPV molecular variants that differ in the length, number and arrangement of deletions in the CP. Population genetic analyses showed significant variation among isolates from pear and apple trees, between isolates from the same host species and, more interestingly, within isolates, supporting the existence of significant levels of variability within individual hosts, as expected by a quasispecies population structure. In addition, different tests support that selection might have been an important force driving diversification within isolates: positive selection was found acting upon certain amino acids. Phylogenetic analyses also showed that isolates did not classify according to the host species (pear or apple trees) but according to the pattern of deletions, suggesting a possible role for deletions during clade diversification., This study was supported by project no. 2011/03/B/NZ9/01680 from National Science Centre of Poland. Work in Valencia was supported by grant BFU2015-65037-P (Ministerio de Ciencia, Innovación y Universidades - FEDER)., Peer reviewed

This article belongs to the Special Issue The Complexity of the Potyviral Interaction Network., Complex systems exhibit critical thresholds at which they transition among alternative phases. Complex systems theory has been applied to analyze disease progression, distinguishing three stages along progression: (i) a normal noninfected state; (ii) a predisease state, in which the host is infected and responds and therapeutic interventions could still be effective; and (iii) an irreversible state, where the system is seriously threatened. The dynamical network biomarker (DNB) theory sought for early warnings of the transition from health to disease. Such DNBs might range from individual genes to complex structures in transcriptional regulatory or protein–protein interaction networks. Here, we revisit transcriptomic data obtained during infection of tobacco plants with tobacco etch potyvirus to identify DNBs signaling the transition from mild/reversible to severe/irreversible disease. We identified genes showing a sudden transition in expression along disease categories. Some of these genes cluster in modules that show the properties of DNBs. These modules contain both genes known to be involved in response to pathogens (e.g., ADH2, CYP19, ERF1, KAB1, LAP1, MBF1C, MYB58, PR1, or TPS5) and other genes not previously related to biotic stress responses (e.g., ABCI6, BBX21, NAP1, OSM34, or ZPN1)., This research was funded by Spain Agencia Estatal de Investigación—FEDER, grant number BFU201565037-P, and by Generalitat Valenciana, grant number PROMETEU/2019/012., Peer reviewed

Predicting viral emergence is difficult due to the stochastic nature of the underlying processes and the many factors that govern pathogen evolution. Environmental factors affecting the host, the pathogen and the interaction between both are key in emergence. In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in their environments. A broad knowledge of these factors will allow better estimating where and when viral emergence is more likely to occur. Here, we investigate how the population structure for susceptibility-to-infection genes of the plant Arabidopsis thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have evolved TuMV lineages in two radically different host population structures: (1) a metapopulation subdivided into six demes (subpopulations); each one being composed of individuals from only one of six possible A. thaliana ecotypes and (2) a well-mixed population constituted by equal number of plants from the same six A. thaliana ecotypes. These two populations were evolved for twelve serial passages. At the end of the experimental evolution, we found faster adaptation of TuMV to each ecotype in the metapopulation than in the well-mixed heterogeneous host populations. However, viruses evolved in well-mixed populations were more pathogenic and infectious than viruses evolved in the metapopulation. Furthermore, the viruses evolved in the demes showed stronger signatures of local specialization than viruses evolved in the well-mixed populations. These results illustrate how the genetic diversity of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen., Work was supported by Spain’s Agencia Estatal de Investigación—FEDER grant BFU2015-65037-P and Generalitat Valenciana grant GRISOLIA/2018/005 to S.F.E. R.G. was supported by Spain’s Agencia Estatal de Investigación pre-doctoral contract BES-2016-077078., Peer reviewed

We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organized around degenerate Bogdanov–Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner., The research leading to these results has received funding from ‘la Caixa’ Foundation. This work has been also partially funded by the ‘María de Maeztu’ Programme for Units of Excellence in R&D (MDM-2014-0445), as well as from projects MTM2014-52209-C2-1-P and MTM2017-86795-C3-1-P from the Spanish MINECO, and from the CERCA Programme of the Generalitat de Catalunya. M.H. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 707658. Work in València was supported by Spain’s Agencia Estatal de Investigación - FEDER grant no. BFU2015-65037-P to S.F.E. J.S. has been also funded by a ‘Ramón y Cajal’ Fellowship (RYC-2017-22243)., Peer reviewed

Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidence from distributions of mutations and from viral RNA amplification suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) mode. Although previous theoretical work has focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, little is known in terms of the bifurcations and transitions involving the so-called error threshold (mutation-induced dominance of mutants) and lethal mutagenesis (extinction of all sequences due to mutation accumulation and demographic stochasticity). Here we analyze a dynamical system describing the intracellular amplification of viral RNA genomes evolving on a single-peak fitness landscape focusing on three cases considering neutral, deleterious, and lethal mutants. We analytically derive the critical mutation rates causing lethal mutagenesis and error threshold, governed by transcritical bifurcations that depend on parameters α (parameter introducing the mode of replication), replicative fitness of mutants (k1), and on the spontaneous degradation rates of the sequences (ϵ). Our results relate the error catastrophe with lethal mutagenesis in a model with continuous populations of viral genomes. The former case involves dominance of the mutant sequences, while the latter, a deterministic extinction of the viral RNAs during replication due to increased mutation. For the lethal case the critical mutation rate involving lethal mutagenesis is µc = 1−ε √α. Here, the SMR involves lower critical mutation rates, being the system more robust to lethal mutagenesis replicating closer to the GR mode. This result is also found for the neutral and deleterious cases, but for these later cases lethal mutagenesis can shift to the error threshold once the replication mode surpasses a threshold given by √α = €/k1., The research leading to these results has received funding from “la Caixa” Foundation and from a Ministerio de Economia y Competitividad grant awarded to the Barcelona Graduate School of Mathematics (BGSMath) under the “María de Maeztu” Program (grant MDM-2014-0445). JS has been also funded by a Ramón y Cajal Fellowship (RYC-2017-22243). JS and TA have been partially funded by the CERCA Programme of the Generalitat de Catalunya. JTL has been partially supported by the MINECO/FEDER grant MTM2015-65715-P, by the Catalan grant 2014SGR-504 and by the Russian Scientific Foundation grants 14-41-00044 and 14-12-00811. TA is also supported by the AGAUR (grant 2014SGR-1307) and the MINECO (grant MTM2015-71509-C2-1-R). SFE has been supported by MINECO-FEDER grant BFU2015-65037-P and by Generalitat Valenciana grant PROMETEOII/2014/021., Peer reviewed

Open Access CAAS Agricultural Journals., Tomato black ring virus (TBRV) infects a wide range of economically important plants, and is distributed worldwide. TBRV is transmitted by soil-inhabiting nematodes. However, a long-distance dispersion is possible via seeds and pollen. In this study, we provided evidence that virus can be efficiently transmitted through tomato seeds. Three tomato varieties (Beta Lux, Grace and Money Maker) and four genetically diverse TBRV isolates collected originally from different hosts were used in the experiments. The seedlings were grown in an insect-proof glasshouse and the presence of TBRV was verified by immunoassay (ELISA). The seed transmission was significantly dependent on tomato cultivar and virus isolate ranging from 1.69% up to 14.57%. Bioassays using Chenopodium quinoa plants confirmed the presence of infectious virus in the seeds., Supported by by the National Science Centre of Poland, Project Nos 2013/11/B/NZ9/02510 and 2017/25/B/NZ9/01715, and by the Spain’s Agencia Estatal de Investigación – FEDER, Grant No. BFU2015-65037-P., Peer reviewed

In this work, we have investigated the evolutionary dynamics of a generalist pathogen, e.g., a virus population, that evolves toward specialization in an environment with multiple host types. We have particularly explored under which conditions generalist viral strains may rise in frequency and coexist with specialist strains or even dominate the population. By means of a nonlinear mathematical model and bifurcation analysis, we have determined the theoretical conditions for stability of nine identified equilibria and provided biological interpretation in terms of the infection rates for the viral specialist and generalist strains. By means of a stability diagram, we identified stable fixed points and stable periodic orbits, as well as regions of bistability. For arbitrary biologically feasible initial population sizes, the probability of evolving toward stable solutions is obtained for each point of the analyzed parameter space. This probability map shows combinations of infection rates of the generalist and specialist strains that might lead to equal chances for each type becoming the dominant strategy. Furthermore, we have identified infection rates for which the model predicts the onset of chaotic dynamics. Several degenerate Bogdanov–Takens and zero-Hopf bifurcations are detected along with generalized Hopf and zero-Hopf bifurcations. This manuscript provides additional insights into the dynamical complexity of host–pathogen evolution toward different infection strategies., A.N. received funding from the “La Caixa” Foundation and the Mathematics for Industry Network COST Action (No. TD1409). M.G.H. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (Agreement No. 707658). J.S. has been funded by a “Ramón y Cajal” Contract (No. RYC-2017-22243), and by the MINECO Grant (No. MTM2015-71509-C2-1-R) and the Spain’s “Agencia Estatal de Investigación” (AEI) Grant (No. RTI2018-098322-B-I00). L.A. has been supported by the AEI Grant (No. MTM2017-86795-C3-1-P). S.F.E.’s support comes from the AEI-FEDER Grant (No. BFU2015-65037-P) and Generalitat Valenciana Grant (No. PROMETEU/2019/012). The research leading to these results has received funding from the “la Caixa” Foundation, from a MINECO grant awarded to the Barcelona Graduate School of Mathematics (BGSMath) under the “María de Maeztu” Program (Grant No. MDM-2014-0445), and from the CERCA Programme of the Generalitat de Catalunya., Peer reviewed

Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to turnip mosaic potyvirus, with a more efficient response against the ancestral isolate. In wild-type plants, both isolates induced similar levels of cytosine methylation changes, including in and around transposable elements and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host., This work was supported by Spain Ministerio de Ciencia e Innovación—FEDER (Grant Nos. BFU2015-65037-P and AGL2016-79825-R to S.F.E. and G.G., respectively) and Generalitat Valenciana (Grant No. PROMETEU/2019/012 to S.F.E.). R.L.C. was supported by a fellowship from the Brazilian funding agency CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico Brasil, Grant No. 200052/2017-9) for the stay in València and from EMBO/EuropaBio (Grant No. 7548) for the stay in Cambridge., Peer reviewed

Viruses are thought to be the ultimate parasites, using host resources for multiplication. Interestingly, many viruses also have their own 'parasites', such as defective interfering RNAs (DI RNAs). One of the plant viruses whose infection can be accompanied by subviral RNAs is the Tomato black ring virus (TBRV). DI RNAs associated with the TBRV genome were generated de novo as a result of prolonged passages in one host. DI RNAs modulate the TBRV accumulation and the severity of the symptoms induced on the infected plants. In this study, we have addressed the question of whether DI RNAs can also affect TBRV vertical transmission through seeds. The experiments were conducted using the TBRV-Pi isolate and Chenopodium quinoa plants. C. quinoa plants were infected with TBRV-Pi with and without DI RNAs. Overall, 4 003 seeds were tested, and the analysis showed that the presence of DI RNAs made the TBRV-Pi seed transmission 44.76% more efficient. Moreover, for the first time, we showed that DI RNAs are being transferred from generation to generation., Supported by the National Science Center in Poland, Project Nos 2013/11/B/NZ9/02510 and 2017/25/B/NZ9/01715. Work in València was supported by the Spain Ministerio de Ciencia e Innovación – FEDER, Project No. BFU2015-65037-P., Peer reviewed

Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations., This work was funded by Spain's Agencia Estatal de Investigación-FEDER grant BFU2015-65037-P and Generalitat Valenciana grant PROMETEU2019/012 to S.F.E. R.G. and A.B. were supported by Ministerio de Ciencia, Innovación y Universidades-FEDER contract BES-2016-077078 and Generalitat Valenciana grant GRISOLIAP/2018/005, respectively., Peer reviewed

Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes., This work was supported by Spain’s Ministerio de Ciencia e Innovación-FEDER Grant PID2019-103998GB-I00 and by Generalitat Valenciana Grants GRISOLIA/2018/005 and PROMETEU2019/012 to S.F.E. R.G. was supported by Ministerio de Ciencia e Innovación-FEDER contract BES-2016-077078. M.P.S.R. was supported by a Young Investigators fellowship from the Universitat de València International 0.7 Cooperation Program., Peer reviewed

The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. We propose that the definition of prion should be expanded, to include the inducible transmissible entities undergoing autocatalytic conversion and consisting of RNA rather than protein. We show that when seen in this framework, some naturally occurring RNAs, including ribozymes, riboswitches, viroids, viroid-like retroelements, and PIWI-interacting RNAs (piRNAs), possess several of the characteristic properties of prions., A.R.M. is a Program Director at the National Science Foundation (NSF), an agency of the U.S. Government; his work was supported by the NSF’s Independent Research/Development and Long-Term Professional Development Programs, but the statements and opinions expressed herein are made in the personal capacity and do not constitute the endorsement by NSF or the government of the United States. S.F.E. was supported by grants BFU2015-65037-P (Spain Agencia Estatal de Investigación-FEDER) and PROMETEOII/2014/012 (Generalitat Valenciana)., Peer reviewed

Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution., This work was supported by grants to SMG and WLD from the US Department of
Agriculture Specialty (USDA) Crop Research Initiative (2009-51181-05894 and 2014-51181-22373), the UK Biotechnology and Biological Sciences Research Council (BBSRC) (grant #BB/L011840/1), as part of the joint USDA-National Science Foundation-National Institutes of Health BBSRC Ecology and Evolution of Infectious Diseases program, and the USDA National Institute of Food and Agriculture (Hatch project number 1017940). WLD was partially supported by a State University of New York (SUNY) Graduate Diversity Fellowship and by a 2014/2015 National Potato
Council scholarship. SFE was supported by Spain Ministerio de Ciencia e Innovacion – FEDER grant BFU2015-65037-P and Generalitat Valenciana grant PROMETEOII/2014/012. DK was financially supported by the Slovenian Research Agency (research core funding No. P4-0407 and research project No. Z1-9158)., Peer reviewed

Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts’ gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whose expression depends on whether hosts were infected with more or less specialized viral strains. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with Turnip mosaic potyvirus strains with different past evolutionary histories and that shown different degrees of specialization. Three disease-related traits were measured and associated with different sets of host genes for each strain. The genetic architectures of these traits differed among viral strains and, in the case of the more specialized virus, also varied along the duration of infection. While most of the mapped loci were strain specific, one shared locus was mapped for both strains, a disease-resistance TIR-NBS-LRR class protein. Likewise, only putative cysteine-rich receptor-like protein kinases were involved in all three traits. The impact on disease progress of 10 selected genes was validated by studying the infection phenotypes of loss-of-function mutant plants. Nine of these mutants have altered the disease progress and/or symptoms intensity between both strains. Compared to wild-type plants six had an effect on both viral strains, three had an effect only on the more specialized, and two were significant during infection with the less specialized., Work was funded by Spain’s Ministerio de Ciencia e Innovación-FEDER grant PID2019-103998GB-I00 and Generalitat Valenciana grants GRISOLIAP/2018/005 and PROMETEU2019/012 to SFE. RG was supported Ministerio de Ciencia e Innovación-FEDER contract BES-2016-077078. MPSR was supported by a Young Investigators fellowship from the Universitat de València International 0.7 Cooperation Program., Peer reviewed

Referred to by: David M. McCandlish; System-specificity of genotype-phenotype map structure; Physics of Life Reviews, Volume 39, December 2021, Pages 73-75.-- Michael Manhart, Sebastian Bonhoeffer; The search for universality in evolutionary landscapes; Physics of Life Reviews, Volume 39, December 2021, Pages 76-78.--
Nitash C G, Christoph Adami; Information-theoretic characterization of the complete genotype-phenotype map of a complex pre-biotic world; Physics of Life Reviews, Volume 38, September 2021, Pages 111-114., Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics—cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis., SM: grant FIS2017-89773-P (MINECO/FEDER, EU); “Severo Ochoa” Centers of Excellence to CNB, SEV 2017-0712. JAC: grants FIS2015-64349-P (MINECO/FEDER, EU) and PGC2018-098186-B-I00 (MICINN/FEDER, EU). JA: grant FIS2017-89773-P (MINECO/FEDER, EU); “Severo Ochoa” Centers of Excellence to CNB, SEV 2017-0712. SEA: the Gatsby Charitable Foundation. LA: Foundational Questions Institute (FQXi) and Fetzer Franklin Fund, a donor advised fund of Silicon Valley Community Foundation, for FQXi Grant number FQXi-RFP-IPW-1913, Stanford Center for Computational, Evolutionary and Human Genomics and the Morrison Institute for Population and Resources Studies, Stanford University, the 2015 Information Processing in Cells and Tissues Conference, and the Mathematical Biosciences Institute at The Ohio State University, for its support through National Science Foundation Award #DMS 0931642. PC: Ramón Areces Postdoctoral Fellowship. RDU: grant BFU2015-67302-R (MINECO/FEDER, EU). SFE: grants BFU2015-65037-P (MCIU-FEDER) and PROMETEOII/2014/012 (Generalitat Valenciana). JK: DFG within CRC1310 “Predictability in Evolution”. NSM: Gates Cambridge Scholarship; Winton Programme for the Physics of Sustainability. JLP: Swiss National Science Foundation, grant PP00P3_170604. MJT: grants EP/L016494/1 (EPSRC/BBSRC Centre for Doctoral Training in Synthetic Biology) and BB/L01386X/1 (BBSRC/EPSRC Synthetic Biology Research Centre, BrisSynBio). MW: the EPSRC and the Gatsby Charitable Foundation., Peer reviewed