1. Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus YDenis Kutnjak, Santiago F. Elena, Maja Ravnikar, 2017, original scientific article Abstract: 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 variations 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 salicylic acid).
IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
Keywords: Potato virus Y, experimental evolution, genetic drift, natural selection, sRNA deep sequencing
Published in DiRROS: 24.07.2024; Views: 144; Downloads: 66
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2. Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant developmentEdgardo Brigatti, Rubén González, Anamarija Butković, Mark Paul Selda Rivarez, Santiago F. Elena, 2020, original scientific article Abstract: 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.
Published in DiRROS: 23.07.2024; Views: 115; Downloads: 98
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3. Transmission modes affect the population structure of potato virus Y in potatoWashington da Silva, Denis Kutnjak, Yi Xu, Yimin Xu, James Giovannoni, Santiago F. Elena, Stewart Gray, 2020, original scientific article Abstract: 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.
Published in DiRROS: 22.07.2024; Views: 122; Downloads: 130
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4. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by subgroup 2 R2R3-MYBs in grapevineLuis Orduña, Miaomiao Li, David Navarro-Payá, Chen Zhang, A. Santiago, Pablo Romero, Živa Ramšak, Gabriele Magon, Janine Höll, Patrick Merz, Kristina Gruden, Alessandro Vannozzi, Dario Cantu, Jochen Bogs, Darren C. J. Wong, Shao-shan Carol Huang, José Tomás Matus, 2022, original scientific article Abstract: The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
Keywords: secondary metabolism, regulatory networks, transcription factors, transcriptional regulation, DNA affinity purification sequencing
Published in DiRROS: 16.07.2024; Views: 118; Downloads: 119
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5. Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistanceRégis L. Corrêa, Denis Kutnjak, Silvia Ambrós, Mónica Bustos, Santiago F. Elena, 2024, original scientific article Abstract: Background: Plant responses to a wide range of stresses are known to be regulated by epigenetic mechanisms. Path-ogen-related investigations, particularly against RNA viruses, are however scarce. It has been demonstrated that Arabi-dopsis thaliana plants defective in some members of the RNA-directed DNA methylation (RdDM) or histone modi-fication pathways presented differential susceptibility to the turnip mosaic virus. In order to identify genes directly targeted by the RdDM-related RNA Polymerase V (POLV ) complex and the histone demethylase protein JUMONJI14 (JMJ14) during infection, the transcriptomes of infected mutant and control plants were obtained and integrated with available chromatin occupancy data for various epigenetic proteins and marks. Results: A comprehensive list of virus-responsive gene candidates to be regulated by the two proteins was obtained. Twelve genes were selected for further characterization, confirming their dynamic regulation during the course of infection. Several epigenetic marks on their promoter sequences were found using in silico data, raising confidence that the identified genes are actually regulated by epigenetic mechanisms. The altered expression of six of these genes in mutants of the methyltransferase gene CURLY LEAF and the histone deacetylase gene HISTONE DEACETYLASE 19 suggests that some virus-responsive genes may be regulated by multiple coordinated epigenetic complexes. A temporally separated multiple plant virus infection experiment in which plants were transiently infected with one virus and then infected by a second one was designed to investigate the possible roles of the identified POLV- and JMJ14-regulated genes in wild-type (WT ) plants. Plants that had previously been stimulated with viruses were found to be more resistant to subsequent virus challenge than control plants. Several POLV- and JMJ14-regulated genes were found to be regulated in virus induced resistance in WT plants, with some of them poisoned to be expressed in early infection stages. Conclusions: A set of confident candidate genes directly regulated by the POLV and JMJ14 proteins during virus infection was identified, with indications that some of them may be regulated by multiple epigenetic modules. A sub-set of these genes may also play a role in the tolerance of WT plants to repeated, intermittent virus infections.Keywords Biotic stress, Defense priming, Epigenetics, Histone modifications, Induced resistance, Potyvirus, RNA-directed DNA methylation.
Keywords: biotic stress, defense priming, epigenetics, histone modifications, induced resistance, Potyvirus, RNA-directed DNA methylation
Published in DiRROS: 17.05.2024; Views: 321; Downloads: 949
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6. Lizard host abundances and climatic factors explain phylogenetic diversity and prevalence of blood parasites on an oceanic islandRodrigo Megía-Palma, Gemma Palomar, Javier Martínez, Bernardo Antunes, Katarzyna Dudek, Anamarija Žagar, Nina Guerra Serén, Miguel A. Carretero, Wiesław Babik, Santiago Merino, 2024, original scientific article Abstract: Host abundance might favour the maintenance of a high phylogenetic diversity of some parasites via rapid transmission rates. Blood parasites of insular lizards represent a good model to test this hypothesis because these parasites can be particularly prevalent in islands and host lizards highly abundant. We applied deep amplicon sequencing and analysed environmental predictors of blood parasite prevalence and phylogenetic diversity in the endemic lizard Gallotia galloti across 24 localities on Tenerife, an island in the Canary archipelago that has experienced increasing warming and drought in recent years. Parasite prevalence assessed by microscopy was over 94%, and a higher proportion of infected lizards was found in warmer and drier locations. A total of 33 different 18s rRNA parasite haplotypes were identified, and the phylogenetic analyses indicated that they belong to two genera of Adeleorina (Apicomplexa: Coccidia), with Karyolysus as the dominant genus. The most important predictor of between-locality variation in parasite phylogenetic diversity was the abundance of lizard hosts. We conclude that a combination of climatic and host demographic factors associated with an insular syndrome may be favouring a rapid transmission of blood parasites among lizards on Tenerife, which may favour the maintenance of a high phylogenetic diversity of parasites.
Keywords: Canary Islands, climate change, next-generation sequencing, phylogenetic analyses, zoology, ecology
Published in DiRROS: 16.05.2024; Views: 246; Downloads: 339
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7. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beechMarjana Westergren, Juliette Archambeau, Marko Bajc, Rok Damjanić, Adélaïde Theraroz, Hojka Kraigher, Sylvie Oddou-Muratorio, Santiago C. González-Martínez, 2023, original scientific article Abstract: Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
Keywords: climate change, Fagus sylvatica, heritability, in situ adaptation, response to selection, selection gradients
Published in DiRROS: 12.12.2023; Views: 442; Downloads: 211
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8. Between but not within-species variation in the distribution of fitness effectsJennifer James, Chedly Kastallya, Katharina Budde, Santiago C. González-Martínez, Pascal Milesi, Tanja Pyhäjärvi, Martin Lascoux, 2023, original scientific article Abstract: New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
Keywords: DFE, deleterious mutations, population structure, forest trees
Published in DiRROS: 12.12.2023; Views: 530; Downloads: 198
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9. Forest genetic resources and forest reproductive material at the crosssection of multiple policy domains in EuropeTodora Rogelja, Laura Secco, Aurelio Padovezi, Davide Pettenella, Mauro Masiero, Elena Pisani, Jacopo Giacomoni, Riccardo Da Re, Sofia Caiolo, Marko Lovrić, Anna-Maria Farsakoglou, Michele Bozzano, François Lefèvre, Bruno Fady, Aurore Desgroux, Santiago C. González-Martínez, Ulla Ovaska, Mari Rusanen, Egbert Beuker, Katriina Soini, Anže Japelj, Konrad Heino, Martin Braun, Erik Dahl Kjær, Jon Kehlet Hansen, Georgeta Mihai, Alin Alexandru, Ecaterina-Nicoleta Apostol, Alicia Fernandez Calvo, Laura Maria Luquero Ramos, Mariano Navarro De La Cruz, Giovanna Ottaviani Aalmo, Bent Leonhard, 2023, published scientific conference contribution Keywords: forest genetic diversity, forest biodiversity, sustainable forest management, policy gap analysis, forest genetic resources, forest reproductive material
Published in DiRROS: 05.10.2023; Views: 670; Downloads: 204
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10. Gene sequence variation data for the publication "Synchronous effective population size changes and genetic stability of forest trees through glacial cycles" : version 1.0Tanja Pyhäjärvi, Francesca Bagnoli, Katharina Budde, Stephen Cavers, Sandra Cervantes, Benjamin Dauphin, Bruno Fady, Patricia Faivre-Rampant, Santiago C. González-Martínez, Delphine Grivet, Felix Gugerli, Véronique Jorge, Chedly Kastallya, Martin Lascoux, Isabelle Lesur Kupin, Pascal Milesi, Dario I. Ojeda, Sanna Olsson, Lars Opgenoorth, Sara Pinosio, Christophe Plomion, Christian Rellstab, Odile Rogier, Simone Scalabrin, Ivan Scotti, Giovanni G Vendramin, Marjana Westergren, 2023, complete scientific database of research data Abstract: This dataset contains the gene sequence variation data (vcf files and their tbi index files) of seven forest tree species used in the manuscript "Synchronous effective population size changes and genetic stability of forest trees through glacial cycles". For each species, between 411 and 651 genotyped trees are included, sampled across Europe in at least 20 locations. Several versions are provided. Species included: Pinus sylvestris, Picea abies, Fagus sylvatica, Populus nigra, Quercus petraea, Pinus pinaster, Betula pendula
Keywords: gene sequence, variation data, data set
Published in DiRROS: 07.03.2023; Views: 772; Downloads: 794
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