In the 'Rocket Science' project, storage of Eruca sativa (salad rocket) seeds for six months on board the International Space Station resulted in delayed seedling establishment. Here we investigated the physiological and molecular mechanisms underpinning the spaceflight effects on dry seeds. We found that 'Space' seed germination vigor was reduced, and ageing sensitivity increased, but the spaceflight did not compromise seed viability and the development of normal seedlings. Comparative analysis of the transcriptomes (using RNAseq) in dry seeds and upon controlled artificial ageing treatment (CAAT) revealed differentially expressed genes (DEGs) associated with spaceflight and ageing. DEG categories enriched by spaceflight and CAAT included transcription and translation with reduced transcript abundances for 40S and 60S ribosomal subunit genes. Among the 'spaceflight-up' DEGs were heat shock proteins (HSPs), DNAJ-related chaperones, a heat shock factor (HSFA7a-like), and components of several DNA repair pathways (e.g., ATM, DNA ligase 1). The 'response to radiation' category was especially enriched in 'spaceflight-up' DEGs including HSPs, catalases, and the transcription factor HY5. The major finding from the physiological and transcriptome analysis is that spaceflight causes vigor loss and partial ageing during air-dry seed storage, for which space environmental factors and consequences for seed storage during spaceflights are discussed.

• Klíčová slova
• climate change, food security, low Earth orbit, salad rocket (Eruca sativa), seed ageing, seed germination, seed storage, seed vigor, seeds in space, spaceflight transcriptomes,
• Publikační typ
• časopisecké články MeSH

Seed predation is an important component of seed mortality of weeds in agro-ecosystems, but the agronomic use and management of this natural weed suppression is hampered by a lack of insight in the underlying ecological processes. In this paper, we investigate whether and how spatial and temporal variation in activity-density of granivorous ground beetles (Coleoptera: Carabidae) results in a corresponding pattern of seed predation. Activity-density of carabids was measured by using pitfall traps in two organic winter wheat fields from March to July 2004. Predation of seeds (Capsella bursa-pastoris, Lamium amplexicaule, Poa annua and Stellaria media) was assessed using seed cards at the same sites and times. As measured by pitfall traps, carabids were the dominant group of insects that had access to the seed cards. In the field, predation of the four different species of seed was in the order: C. bursa-pastoris>P. annua>S. media>L. amplexicaule; and this order of preference was confirmed in the laboratory using the dominant species of carabid. On average, seed predation was higher in the field interior compared to the edge, whereas catches of carabids were highest near the edge. Weeks with elevated seed predation did not concur with high activity-density of carabids. Thus, patterns of spatial and temporal variation in seed predation were not matched by similar patterns in the abundance of granivorous carabid beetles. The lack of correspondence is ascribed to effects of confounding factors, such as weather, the background density of seeds, the composition of the carabid community, and the phenology and physiological state of the beetles. Our results show that differences in seed loss among weed species may be predicted from laboratory trials on preference. However, predator activity-density, as measured in pitfall traps, is an insufficient predictor of seed predation over time and space within a field.

• MeSH
• biologické modely MeSH
• brouci fyziologie   MeSH
• časové faktory MeSH
• demografie MeSH
• populační dynamika MeSH
• predátorské chování fyziologie   MeSH
• semena rostlinná * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Nizozemsko MeSH

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory.

• MeSH
• biodiverzita * MeSH
• biologické modely * MeSH
• fyziologie rostlin * MeSH
• kvantitativní znak dědičný * MeSH
• stromy fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

Intensified agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies, however, have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continental-wide study, we assess how functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation at the field scale. We found that ecosystem functions are vulnerable to disturbances in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.

• Klíčová slova
• arable plants, carabids, ecosystem services, hierarchical modelling of species communities,
• MeSH
• biodiverzita MeSH
• ekosystém * MeSH
• predátorské chování * MeSH
• semena rostlinná MeSH
• zemědělství MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Climate change is leading to species redistributions. In the tundra biome, shrubs are generally expanding, but not all tundra shrub species will benefit from warming. Winner and loser species, and the characteristics that may determine success or failure, have not yet been fully identified. Here, we investigate whether past abundance changes, current range sizes and projected range shifts derived from species distribution models are related to plant trait values and intraspecific trait variation. We combined 17,921 trait records with observed past and modelled future distributions from 62 tundra shrub species across three continents. We found that species with greater variation in seed mass and specific leaf area had larger projected range shifts, and projected winner species had greater seed mass values. However, trait values and variation were not consistently related to current and projected ranges, nor to past abundance change. Overall, our findings indicate that abundance change and range shifts will not lead to directional modifications in shrub trait composition, since winner and loser species share relatively similar trait spaces.

• MeSH
• ekosystém * MeSH
• fenotyp MeSH
• klimatické změny MeSH
• semena rostlinná MeSH
• tundra * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

INTRODUCTION: Analysis of aboveground vegetation and soil seed bank is an important source of data on the state and dynamics of vegetation. It is especially important in landscapes exposed to disturbances, which have lost their functions. For our research, a post-mining area in the region of the Upper Silesian Black Coal Basin was selected, whose relief and ecosystems are strongly disturbed by underground mining and are currently also affected by ongoing climate change. METHOD: Data collection for our research took place in the territory of two waterlogged subsidence basins in the Karvina region, Czech Republic. We evaluated 30 phytosociological releves using techniques of Zurich - Montpellier school and 540 soil cores using cultivation and extraction method. RESULTS: In the above-ground vegetation, 115 plant species were identified. By cultivating soil samples, we determined 60 species from 1,487 seedlings, by extraction method 66 species from 5,999 seeds. A statistically significant effect of the presence of the tree layer on the number of species obtained by the extraction method was demonstrated. There is also a statistically significant difference between the selected analysis methods in terms of the length of the captured seeds and their seed mass. DISCUSSION: The construction of a rarefaction curve demonstrated that the use of cultivation and extraction methods leads to a greater capture of soil seed bank species. The similarity between the species composition of aboveground vegetation and the soil seed bank correspond to similarities observed in other studies from degraded habitats. Very low similarity between the species of the soil seed bank from cultivation and extraction method is probably caused by the highly variable distribution of seeds in the soil in time and space.

• Klíčová slova
• above-ground vegetation, cultivation method, extraction method, post-mining landscape, similarity of species composition, soil seed bank,
• Publikační typ
• časopisecké články MeSH

Cycads are ancient seed plants (gymnosperms) that emerged by the early Permian. Although they were common understory flora and food for dinosaurs in the Mesozoic, their abundance declined markedly in the Cenozoic. Extant cycads persist in restricted populations in tropical and subtropical habitats and, with their conserved morphology, are often called 'living fossils.' All surviving taxa receive nitrogen from symbiotic N2-fixing cyanobacteria living in modified roots, suggesting an ancestral origin of this symbiosis. However, such an ancient acquisition is discordant with the abundance of cycads in Mesozoic fossil assemblages, as modern N2-fixing symbioses typically occur only in nutrient-poor habitats where advantageous for survival. Here, we use foliar nitrogen isotope ratios-a proxy for N2 fixation in modern plants-to probe the antiquity of the cycad-cyanobacterial symbiosis. We find that fossilized cycad leaves from two Cenozoic representatives of extant genera have nitrogen isotopic compositions consistent with microbial N2 fixation. In contrast, all extinct cycad genera have nitrogen isotope ratios that are indistinguishable from co-existing non-cycad plants and generally inconsistent with microbial N2 fixation, pointing to nitrogen assimilation from soils and not through symbiosis. This pattern indicates that, rather than being ancestral within cycads, N2-fixing symbiosis arose independently in the lineages leading to living cycads during or after the Jurassic. The preferential survival of these lineages may therefore reflect the effects of competition with angiosperms and Cenozoic climatic change.

• MeSH
• cykasy MeSH
• dusík MeSH
• izotopy dusíku MeSH
• sinice * MeSH
• symbióza * MeSH
• zkameněliny MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• dusík MeSH
• izotopy dusíku MeSH

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

• MeSH
• buněčné jádro genetika   MeSH
• centromera genetika   MeSH
• chromatin genetika   metabolismus   MeSH
• chromozomy rostlin genetika   MeSH
• genetická variace MeSH
• genom rostlinný genetika   MeSH
• genomika MeSH
• haplotypy genetika   MeSH
• ječmen (rod) genetika   MeSH
• mapování chromozomů MeSH
• meióza genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• semena rostlinná genetika   MeSH
• umělé bakteriální chromozomy genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• chromatin MeSH

BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.

• Klíčová slova
• Allele Catalog Pipeline, Allele Catalog Tool, Alleles in Gene, Data Visualization, Variant Calling Pipeline,
• MeSH
• alely * MeSH
• Arabidopsis * genetika   MeSH
• data mining * metody   MeSH
• datové soubory jako téma * MeSH
• frekvence genu MeSH
• genotyp MeSH
• Glycine max * genetika   MeSH
• internet * MeSH
• kukuřice setá * genetika   MeSH
• metadata MeSH
• mutace MeSH
• pigmentace genetika   MeSH
• rostlinné geny genetika   MeSH
• software * MeSH
• substituce aminokyselin MeSH
• vegetační klid genetika   MeSH
• vizualizace dat MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DOG1 protein, Arabidopsis MeSH Prohlížeč

Carabids are considered beneficial arthropods in agroecosystems, where they prey on crop pests or consume weed seeds. Therefore, knowledge of the spatial distribution of carabids in agricultural landscapes is crucial to efficiently manage the ecosystem services that they provide. In the present study, we investigated the spatial distribution of carabids around arable field-woodlot boundaries in different seasons: (1) early spring, (2) late spring, (3) summer and (4) late autumn. The spatial distribution of carabid abundance (activity-density) and species richness varied seasonally, and the total abundance was highest within arable fields, except in early spring when it peaked at the boundaries. The observed pattern was mainly driven by the spatial distribution of the open-habitat species, which aggregated near the field boundaries during winter and early spring. The open-habitat species penetrated into woodlots during the summer season but occurred almost exclusively outside woodlots in the other sampling periods. The abundance of the forest species was highest within woodlots with the exception of the early spring season, when their abundance peaked at the boundaries. Carabid species richness was highest within arable fields in close proximity to woodlot boundaries with the exception of the summer season, when the total species richness was similar across habitats.

• MeSH
• biodiverzita * MeSH
• brouci * MeSH
• časoprostorová analýza * MeSH
• ekosystém * MeSH
• populační dynamika MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH