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Povzetek: Background: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. Results: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. Conclusions: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies.
Ključne besede: tomato, weed, virus, viroid, virome, virus discovery, virus diversity, phylogenetics, metagenomics, viromics
Objavljeno v DiRROS: 13.04.2023; Ogledov: 738; Prenosov: 173
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Povzetek: Purpose of Review Recognizing that in the context of global change, tree genetic diversity represents a crucial resource for future forest adaptation, we review and highlight the major forest genetics research achievements of the past decades in biodiversity-rich countries of the Mediterranean region. For this, we conducted a bibliometric analysis of the scientific literature spanning the past thirty years (1991–2020). Putting together the representative regionwide expertise of our co-authorship, we propose research perspectives for the next decade. Recent Findings Forest genetics research in Mediterranean countries is organized into three different scientific domains of unequal importance. The domain “Population diversity and Differentiation” related to over 62% of all publications of the period, the domain “Environmental conditions, growth and stress response” to almost 23%, and the domain “Phylogeography” to almost 15%. Citation rate was trending the opposite way, indicating a strong and sustained interest in phylogeography and a rising interest for genetics research related to climate change and drought resistance. The share of publications from Asia and Africa to the total within the Mediterranean increased significantly during the 30-year period analyzed, reaching just below 30% during the last decade. Summary Describing poorly known species and populations, including marginal populations, using the full potential of genomic methods, testing adaptation in common gardens, and modeling adaptive capacity to build reliable scenarios for forest management remain strategic research priorities. Delineating areas of high and low genetic diversity, for conservation and restoration, respectively, is needed. Joining forces between forest management and forest research, sharing data, experience, and knowledge within and among countries will have to progress significantly, e.g., to assess the potential of Mediterranean genetic resources as assisted migration material worldwide.
Ključne besede: conservation ·, forest genetic resources, genetic diversity, global change, Mediterranean, sustainable management
Objavljeno v DiRROS: 09.12.2022; Ogledov: 587; Prenosov: 313
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Ključne besede: conservation biological control, pest control, functional diversity
Objavljeno v DiRROS: 06.09.2022; Ogledov: 585; Prenosov: 288
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Povzetek: Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of “Genomics and Adaptation in Forest Ecosystems” brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.
Ključne besede: gene conservation, genetic diversity, local adaptation, pathogens, selection, mycorrhizal fungi
Objavljeno v DiRROS: 18.02.2022; Ogledov: 774; Prenosov: 557
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Povzetek: Ectomycorrhizal communities are rarely studied on seasonal basis, especially in poplar plantations. In this study we analysed the ectomycorrhizal community in a mature twenty-year-old white poplar (Populus alba L.) plantation during four consecutive seasons. Using morpho-anatomical and molecular identification 30 taxa of ectomycorrhizal fungi were recorded of which 15 were identified to the species level, 12 to the genus level, 2 to the family, and one morphotype of ectomycorrhizae remained unidentified. The most abundant among identified ectomycorrhizal fungi were: Inocybe griseovelata, Inocybe splendens, Tuber rufum, and Tomentella sp. 2, which together represented up to 50% of all ectomycorrhizal root tips. The number of ectomycorrhizal fungal taxa and the percentage of vital ectomycorrhizal root tips were highest in winter and spring, respectively. The diversity indices of ectomycorrhizae, number of vital ectomycorrhizal root tips, and total fine roots in the studied poplar plantation did not differ between seasons. Ectomycorrhizal fungi belonging to Inocybaceae family and the short-distance exploration strategy were dominant in all four seasons. On the other hand, the abundance of ectomycorrhizal root tips belonging to the medium-distance exploration strategy type was significantly higher in spring in comparison with autumn and winter.
Ključne besede: Populus alba L., Ectomycorrhizal diversity, morpho-anatomical characterization, molecular identification, seasons
Objavljeno v DiRROS: 03.12.2021; Ogledov: 956; Prenosov: 465
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