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opencc-by-4.0Oct 2022View details →

The N-terminal executioner domains of NLR immune receptors are structurally and functionally conserved across major plant lineages: Extended Data

Raw data and supporting files for an updated version of the manuscript now entitled "The N-terminal executioner domains of NLR immune receptors are structurally and functionally conserved across major plant lineages". Related to an original version of the bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2022.10.19.512840v1

Pollinator visitation on Na-enriched plants in a subalpine meadow

Many plants have evolved nutrient rewards to attract pollinators to flowers, but most research has focused on the sugar content of floral nectar resources. Concentrations of sodium in floral nectar (a micronutrient in low concentrations in nectar) can vary substantially both among and within co-occurring species. Sodium concentrations in floral nectar might play an important and underappreciated role in plant-pollinator interactions, especially because many animals, including pollinators, are sodium-limited in nature. Yet, the consequences of variation in sodium concentrations in floral nectar have gone largely unexplored. Here, we investigate whether enriching floral nectar with sodium influences the composition, diversity, and abundance of pollinator interactions. We experimentally enriched sodium concentrations in four plant species in a subalpine meadow in Colorado, USA. We found that flowers with sodium-enriched nectar received more visits from a greater diversity of pollinator visitors throughout the season. Each pollinator species foraged more frequently on flowers enriched with sodium and showed evidence of other changes to pollinator foraging behavior, including greater dietary evenness. These findings are consistent with the 'salty nectar hypothesis,' providing evidence for the importance of sodium limitation in pollinators and suggesting that even small nectar constituents can shape plant-pollinator interactions.

Summary data for "Young mixed planted forests store more carbon than monocultures: a meta-analysis"

This is the dataset used in "Young mixed planted forests store more carbon than monocultures: a meta-analysis" published in Frontiers in Forests & Global Change. The dataset contains carbon or biomass data for mixed and monoculture planted forests from 21 sites with a global coverage. We provide summary data necessary to conduct a meta-analysis: mean, standard deviation, and sample size, for each unique mixed and monoculture treatment at each study site. We indicate whether the values provided are aboveground carbon or biomass.For each treatment we also provide the species richness, age and species. We provide the longitude, latitude and country for each study site.Our study also assessed the effect of study design (experiment vs existing plantation), species origin (native vs non-native/mixed), and presence of nitrogen fixer in the mixture (N fixer present vs absent), we record the value of each of these factors. Finally, we categorised a subset of monocultures as commercial species monocultures based on the species use in that location.

Tillage agriculture and afforestation threaten tropical savanna plant communities across a broad rainfall gradient in India

The consequences of land-use change for savanna biodiversity remain undocumented in most regions of tropical Asia. One such region is western Maharashtra, India, where old-growth savannas occupy a broad rainfall gradient and are increasingly rare due to agricultural conversion and afforestation. To understand the consequences of land-use change, we sampled herbaceous plant communities of old-growth savannas and three alternative land-use types: tree plantations, tillage agriculture, and agricultural fallows (n=15 sites per type). Study sites spanned 457 to 1954 mm of mean annual precipitation—corresponding to the typical rainfall range of mesic savannas globally. Across the rainfall gradient, we found consistent declines in old-growth savanna plant communities due to land-use change. Local-scale native species richness dropped from a mean of 12 species/m2 in old-growth savannas to 8, 6, and 3 species/m2 in tree plantations, fallows, and tillage agriculture, respectively. Cover of native plants declined from a mean of 49% in old-growth savannas to 27% in both tree plantations and fallows, and 4% in tillage agriculture. Reductions in native cover coincided with increased cover of invasive species in tree plantations (18%), fallows (18%), and tillage agriculture (3%). In analyses of community composition, tillage agriculture was most dissimilar to old-growth savannas, while tree plantations and fallows showed intermediate dissimilarity. These compositional changes were driven partly by the loss of characteristic savanna species: 65 species recorded in old-growth savannas were absent in other land uses. Indicator analysis revealed 21 old-growth species, comprised mostly of native savanna specialists. Indicators of tree plantations (9 species) and fallows (13 species) were both invasive and native species, while the 2 indicators of tillage agriculture were invasive. As reflective of declines in savanna communities, mean native perennial graminoid cover of 27% in old-growth savannas dropped to 9%, 7%, and 0.1% in tree plantations, fallows, and tillage agriculture, respectively. Synthesis: Agricultural conversion and afforestation of old-growth savannas in India destroys and degrades herbaceous plant communities that do not spontaneously recover on fallowed land. Efforts to conserve India's native biodiversity should encompass the country's widespread savanna biome and seek to limit conversion of irreplaceable old-growth savannas.

Relationships between plant species richness and grazing intensity in a semiarid ecosystem

Plant species richness is an important property of ecosystems that is altered by grazing. In a semiarid environment, we tested the hypotheses that (1) small-scale herbaceous plant species richness declines linearly with increasing grazing intensity by large ungulates, (2) precipitation and percent sand interact with grazing intensity, and (3) response of herbaceous plant species richness to increasing intensity of ungulate grazing varies with patch productivity. During January to March 2012, we randomly allocated 50, 1.5-m x 1.5-m grazing exclosures within each of six 2,500 ha study sites across South Texas, USA. We counted the number of herbaceous plant species and harvested vegetation in 0.25-m2 plots within exclosures (ungrazed control plots) and in the grazed area outside the exclosures (grazed treatment plots) during October and November 2012–2019. We estimated percent use (grazing intensity) based on the difference in herbaceous plant standing crop between control plots and treatment plots. We selected the negative binomial regression model that best explained the relationship between grazing intensity and herbaceous plant species richness using the Schwarz Bayesian Information Criterion. After accounting for the positive effect of precipitation and percent sand on herbaceous plant species richness, species richness/0.25 m2 increased slightly from 0 to ~ 30% grazing intensity and then declined with increasing grazing intensity. Linear and quadratic responses of herbaceous plant species richness to increasing grazing intensity were greater for the least productive patches (<15.7 g/0.25 m2) than for productive patches (≥15.7 g/0.25 m2). Our results followed the pattern predicted by the intermediate disturbance hypothesis model for the effect of grazing intensity on small-scale herbaceous plant species richness.

Dataset for "Plant biodiversity limits carbon recapture in warming boreal forests"

See details from the publication "Plant biodiversity limits carbon recapture in warming boreal forests" in Nature Communications Earth & Environment for details on data generation and usage. Columns id - unique identifier plot_id - forest plot where vegetation samples were collected species - sampled plant species name dry_weight - weight of species after fully drying given in grams wet_weight - weight of species immediately after collection given in grams

Plant diversity and soil legacy independently affect the plant metabolome and induced responses following herbivory

Plant and soil biodiversity can have significant effects on herbivore resistance mediated by plant metabolites. Here, we disentangled the independent effects of plant diversity and soil legacy on constitutive and herbivore-induced plant metabolomes of three plant species in two complementary microcosm experiments. First, we grew plants in sterile soil with three different plant diversity levels. Second, single plant species were grown on soil with different plant diversity-induced soil legacies. We infested a subset of all plants with Spodoptera exigua larvae, a generalist leaf-chewing herbivore, and assessed foliar and root metabolomes. Neither plant diversity nor soil legacy had significant effects on overall foliar, root, or herbivore-induced metabolome composition. Herbivore-induced metabolomes, however, differed from those of control plants. We detected 139 significantly regulated metabolites by comparing plants grown in monocultures with conspecifics growing in plant or soil legacy mixtures. Moreover, plant-plant and plant-soil interactions regulated 141 metabolites in herbivore-induced plants. Taken together, plant diversity and soil legacy independently alter the concentration and induction of plant metabolites, thus affecting the plant's defensive capability. This is a first step towards disentangling plant and soil biodiversity effects on herbivore resistance, thereby improving our understanding of the mechanisms that govern ecosystem functioning.

Effects of large mammal exclusion on seedling communities depend on plant species traits and landscape protection in human-modified Costa Rican forests

<ol> <li>Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.</li> <li>We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage, and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established forty seedling plot-pairs, with one plot excluding LTH-mammals and one not, and monitored seedlings of 116 woody species for 26 months.</li> <li>We found significant effects of LTH-mammal exclusion on seedling survival contingent upon the protection of forests at the landscape level and forest stage. After 26 months, survival differences between LTH-mammal exclusion and non-exclusion treatments were greater in protected than unprotected landscapes. Additionally, plant species' traits were related to the LTH-mammals' differential effects, as LTH-mammals reduced the survival of seedlings of larger-seeded species the most. Overall, LTH-mammals' effects translated into significant shifts in community composition as seedling communities inside and outside the exclosures diverged. Moreover, lower density and higher species diversity were found as early as 12 and 18 months outside than inside exclosures.</li> <li> Synthesis and applications. Insight into the interactions between LTH-mammals and seedling communities in forest regeneration can be instrumental in planning effective restoration efforts. We highlight the importance of landscape protection in seedling survival and the role of LTH-mammals in promoting seedling diversity in mature forests but also in secondary successional forests. The findings suggest that conservation efforts and possibly trophic rewilding can be important approaches for preserving diversity and influencing the trajectory of secondary tropical forest succession. However, we also caution that an overabundance of LTH-mammals may adversely impact the pace of forest succession due to their preference for large-seeded species. Therefore, a comprehensive wildlife management plan is indispensable. Additionally, longer-term studies on LTH-mammals are necessary to understand the effects of temporal fluctuations that are undetected in short-term studies.</li> </ol>

Annotated dataset of pollen pellet images from 40 major beekeeping plants

Pollen is the main source of proteins, amino acids, lipids, sterols, fatty acids, vitamins and other nutrients for honeybees. Knowing the pollinating plants of an area and identifying the incoming pollen sources inside the hive can be extremely useful information for beekeepers in controlling the development of their colonies and implementing appropriate manipulations throughout the year. Thus, a database was created, including images and characteristics of the pollen pellets of 40 major beekeeping plants. Bee pollen was collected from pollen traps, which were placed at the hive entrances of experimental bee colonies.Freshly collected pollen was cleaned of foreign matter and placed -18 oC in glass jars until the time of analysis. Every 15 days a representative sample of 10% of the total quantity was separated mainly by color, shape and size in order to assess the contribution of each species. For the identification of pollen grains, the Louveaux method was used, according to which a small amount of pollen was placed on a slide and the pellets were dissolved with 2-3 drops of diethyl ether. After evaporation of the solvent, a drop of aqueous isoglucose solution (2:1) was added to hydrate the pollen grains and a drop of alcoholic fuchsin solution was added to stain them. The preparations were then placed on a hot plate to evaporate the moisture. This was followed by placement of a coverslip with Entellan to fix the preparation. The final preparation was examined under the microscope to identify the plant from which the pollen pellet came. For the microscopic identification of the pollen types, the collection of reference slides from the Laboratory of Apiculture of the Aristotle University of Thessaloniki, which is accredited to ISO 17025:2017, was used. Pollen pellets from the various taxa were placed on a special white plate to ensure a neutral background and to limit possible reflections as much as possible. Photographs were taken with smartphone cameras, in order to simulate the actual conditions of photography for potential users in the field.The dataset contains 139 training captured images of bee pollen pellets from 40 major beekeeping plants (class list can be found below) and 13 testing captured images. Polygon annotations were created using LabelMe software and saved in COCO Annotation format (train.json and val.json files).Further information about the related project (SmartBeeKeep) can be found in the following article and presentation (please site if you use these data):<ul><li>Vasilios Liolios, Dimitrios Kanelis, Maria-Anna Rodopoulou, Chrysoula Tananaki (2023). A Comparative Study of Methods Recording Beekeeping Flora. Forests, 14(8), 1677; <a href="https://doi.org/10.3390/f14081677">https://doi.org/10.3390/f14081677</a> </li><li>Nikos Grammalidis, Andreas Stergioulas, Aggelos Avramidis, Konstantinos Karystinakis, Athanasios Partozis, Athanasios Topaloudis, Georgia Kalantzi, Chrisoula Tananaki, Dimitrios Kanelis, Vasilis Liolios, and Madesis Panagiotis "A smart beekeeping platform based on remote sensing and artificial intelligence", Proc. SPIE 12786, Ninth International Conference on Remote Sensing and Geoinformation of the Environment (RSCy2023), 127860C (21 September 2023); <a href="https://doi.org/10.1117/12.2681866%20">https://doi.org/10.1117/12.2681866</a> Event: Ninth International Conference on Remote Sensing and Geoinformation of the Environment (RSCy2023), 2023, Ayia Napa, Cyprus <a href="https://smartbeekeep.eu/files/rscyp23_sbk_paper.pdf">Author preprint available</a></li></ul>Annotation - Latin nameAnthemis - Anthemis sp.Asphodelus - Asphodelus fistulosusBrassica napus - Brassica napusCastanea sativa - Castanea sativaCephalaria transsylvanica - Cephalaria transsylvanicaChenopodium album - Chenopodium albumCichorium - Cichorium intybusCistus - Cistus creticusCistus salvifolius - Cistus salvifoliusConvolvulus - Convolvulus arvensisDaucus - Daucus carotaEchium - Echium plantagineumErica - Erica manipulifloraHedera helix - Hedera helixHelianthus - Helianthus annuusHeliotropium - Heliotropium europaeumHypericum - Hypericum perforatumLavandula - Lavandula angustifoliaLigustrum - Ligustrum japonicumMatricaria - Matricaria chamomillaOlea_europaea_9cm - Olea europaeaPaliurus - Paliurus spina-christiPapaver - Papaver rhoeasPinus - Pinus sp.Polygonum_aviculare - Polygonum avicularePortulaca - Portulaca oleraceaPyrus - Pyrus spinosaQuercus - Quercus cocciferaRosmarinus - Rosmarinus officinalisRubus - Rubus ulmifoliusCarduus - Silybum marianumsinapis - Sinapis arvensisSonchus - Sonchus asperTaraxacum - Taraxacum officinaleTamarix - Tamarix sp.Tilia - Tilia sp.Tribulus - Tribulus terrestisTrifolium pratensis - Trifolium campestreVerbascum - Verbascum nigrumVicia - Vicia villosa

Plant secondary metabolite increases the control-effectiveness of natural enemy - based on caffeine and Snellenius manilae

The food resources in the field can effectively strengthen the ability of natural enemies to control the pest. Certain compounds, in addition to carbohydrates and amino acids, may improve the physiological performance of insects. Caffeine, for instance, has been shown to enhance pollinator memory and physiological reactions. However, little is known about how caffeine influences parasitoids. The control effectiveness and survival rate of the parasitoid (Snellenius manilae) were tested in this study after the parasitoids were fed solutions with different concentrations of caffeine. We examined caffeine concentrations of 10-2, 10-4, and 10-6 (M) mixed with a 25% sucrose solution and a pure sucrose solution as a control group. The results show that a concentration of 10-6 caffeine solution significantly increased the parasitism rate of S. manilae by 10.76% when compared to the control group. Despite the significantly lower survival rate and male bias of S. manilae offspring in the 10-2 treatment, no further negative responses in growth performance, development time, or cocoon weight were observed. These findings suggest that an appropriate concentration of caffeine solution can have a positive impact on the control effectiveness of parasitoids in the laboratory. Our results highlight the potential of secondary compounds to increase the bio-control effectiveness.

Plant science corpus

The plant science corpus consists of the titles and abstracts of plant science articles in PubMed published prior to 2021 with a small number of 2021 records due to modification of records. The columns are:<ul><li>Index: integer index serving as identifier</li><li>PMID: PubMed identifier</li><li>Date: Publication date</li><li>Journal: journal where the article was published</li><li>Title: Title of the article</li><li>Abstract: Abstract of the article</li><li>Corpus: Title and abstract combined</li><li>Text classification score: plant science record prediction model score</li><li>Preprocessed corpus: Corpus after lower-casing, stop word removal, removal of non-alphanumeric and non-white space characters, lemmitisation</li><li>Topic: index of topics after topic modeling</li></ul>

Effects of disturbance on genetic diversity in the submersed aquatic plant Vallisneria americana

In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River, of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from 5 sites just before the storms with 239 shoots collected from 9 sites four years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.

Data for "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"

This dataset was used to perform the analyses in the manuscript "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"

opencc-zeroDec 2023View details →

Data from: Elevational range sizes of woody plants increase with climate variability in the Tropical Andes

Aim: The climate variability hypothesis proposes that species subjected to wide variation in climatic conditions will evolve wider niches, resulting in larger distributions. We test this hypothesis in tropical plants across a broad elevational gradient; specifically, we use a species-level approach to evaluate whether elevational range sizes are explained by the levels of thermal variability experienced by species. Location: Central Andes Time period: Present day Taxon: Woody plants Methods: Combining data from 479 forest plots, we determined the elevational distributions of nearly 2300 species along an elevational gradient (~209 – 3800 m). For each species, we calculated the maximum annual variation in temperature experienced across its elevational distribution. We used phylogenetic generalized least square models to evaluate the effect of thermal variability on range size. Our models included additional covariates that might affect range size: body size, local abundance, mean temperature and total precipitation. We also considered interactions between thermal variability and mean temperature or precipitation. To account for geometric constraints, we repeated our analyses with a standardized measure of range size, calculated by comparing observed range sizes with values obtained from a null model. Results: Our results supported the main prediction of the climate variability hypothesis. Thermal variability had a strong positive effect on the range size, with species exposed to higher thermal variability having broader elevational distributions. Body size and local abundance also had positive, yet weak effects, on elevational range size. Furthermore, there was a strong positive interaction between thermal variability and mean annual temperature. Main conclusions: Thermal variability had an overriding importance in driving elevational range sizes of woody plants in the Central Andes. Moreover, the relationship between thermal variability and range size might be even stronger in warmer regions, underlining the potential vulnerability of tropical montane floras to the effects of global warming.

opencc-by-4.0Aug 2024View details →

Data for: Detection of oomycete pathogens in UK peat-free growing media and implications for plant health

This dataset on Zenodo accompanies the manuscript Frederickson-Matika et al. (2024), Detection of oomycete pathogens in UK peat-free growing media and implications for plant health. There are two files: <ul> <li>metadata.tsv - plain text table as tab-separated variables</li> <li>raw_data.tar.gz - compressed archive of 43 paired raw FASTQ files</li> </ul> This represents a subset of two complete Illumina MiSeq plates (in two dated folderes) run at the James Hutton Institute containing other environmental samples using the same protocol. Only the synthetic controls and peat-free samples are provided here. To repeat the analysis described in the paper, first install THAPBI PICT. See <a href="https://github.com/peterjc/thapbi-pict/">https://github.com/peterjc/thapbi-pict/ </a>for instructions. At the time of the paper, v1.0.14 was the current release. Next, decompress the raw data into a folder of paired gzipped FASTQ files. There is no need to decompress those: <pre><code> $ tar -zxvf raw_data.tar.gz $ ls -1 plate_20220505/ plate_20230608/</code></pre> If you wish, verify the checksums to confirm the data integrity: <pre><code> $ cd plate_20220505/ $ md5sum -c MD5SUM.txt $ cd ../plate_20230608/   $ md5sum -c MD5SUM.txt $ cd ..</code></pre> Setup output directories: <pre><code><code>   $ mkdir -p intermediate/ summary/</code></code></pre> <pre>Run the THAPBI PICT pipeline:</pre> <pre><code>   $ thapbi_pict pipeline -m 1s3g \ -i plate_*/ -o summary/peat-free \ -y plate_*/GBL*.fastq.gz \ -n plate_*/GBL*.fastq.gz \ -s intermediate/ \ -t metadata.tsv -u \ -x 9 -c 1,2,3,4,5,6,7,8</code> </pre> The options here are as follows: <ul> <li>-i - two input directories of paired raw FASTQ files.</li> <li>-n - negative controls used to increase the absolute abundance threshold</li> <li>-y - synthetic controls used to increase the fractional abundance threshold</li> <li>-s - optional location to store intermediate files</li> <li>-o - output stem for reports</li> <li>-t - filename for tab-separated-variable metadata</li> <li>-u - show unsequenced samples defined in the metadata</li> <li>-x - which metadata column contains Illumina FASTQ filename stems</li> <li>-c - which metadata columns to include in the report.</li> </ul> This assumes the following key default settings: <ul> <li>-a 100 (default absolite abundance threshold)</li> <li>-f 0.001 (default fractional abundance threshold)</li> <li>-d -(default provided ITS1 database).</li> </ul> With these settings, only synthetic sequences were found in the controls, and therefore the thresholds were not automatically increased any further. Opening the output file summary/peat-free.ITS1.samples.1s3g.xlsx in Excel or similar should show you a table resembling Table 1 in the paper, but one row per sequencing sample, and additional columns with per-sample per-species read counts etc.

restrictedIPD-UNDECIDEDFeb 2026View details →

Safety and Immunogenicity of Plant-Derived Pfs25 VLP-FhCMB Malaria Transmission Blocking Vaccine in Healthy Adults

ClinicalTrials.gov study NCT02013687. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Effect of a Plant-Focused Diet on Nutritional Status in Malnourished Peritoneal Dialysis Patients

ClinicalTrials.gov study NCT07157397. IPD Sharing: NO. Countries: 1. Publications: 0.

controlledIPD-YESFeb 2026View details →

Randomized Proof-of-Concept Trial to Evaluate the Safety and Explore the Effectiveness of Resveratrol, a Plant Polyphenol, for COVID-19

ClinicalTrials.gov study NCT04400890. IPD Sharing: YES. Countries: 1. Publications: 2.

closedIPD-NOFeb 2026View details →

Efficacy, Safety, and Immunogenicity of a Plant-Derived Quadrivalent Virus-Like Particles (VLPs) Influenza Vaccine in Adults

ClinicalTrials.gov study NCT03301051. IPD Sharing: NO. Countries: 7. Publications: 1.