Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens

Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for Phytophthora sojae, Globisporangium ultimum, Pythium oligandrum, and G. spinosum. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with Copia-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in P. sojae. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.

Data from: High foraging fidelity and plant-pollinator network dominance of non-native honeybees (Apis mellifera) in the Ecuadorian Andes

These data reflect the floral visitor survey and mark-recapture efforts used in the 2022 study, "High Foraging Fidelity and Plant‑Pollinator Network Dominance of Non‑native Honeybees (Apis mellifera) in the Ecuadorian Andes"

opencc-by-4.0Mar 2024View details →

More than half of the alien plants naturalised in the arid southeast of the Iberian Peninsula could be invasive

Data set of dthe paper "More than half of the alien plants naturalised in the arid southeast of the Iberian Peninsula could be invasive", by María J. Salinas-Bonillo, Alba Rodríguez-Rodríguez, M. Trinidad Torres-García, Miguel Cueto, and Javier Cabello. This data set includes the scores of the Australian and New Zealand Weed Risk Assessment (AWRA) (Pheloung et al. 1999) for 144 alien plant species naturalised in the arid southeast of the Iberian Peninsula, the geographical coordinates where they are recorded in the wild, and the bibliographic sources from which the information was obtained to answer the AWRA questions.

CRISPRi-based circuits to control gene expression in plants

The plasmid data supporting the publication: CRISPRi-based circuits to control gene expression in plants

Data for: Biological mitigation of soil nitrous oxide emissions by plant metabolites

Plant metabolites significantly affect soil nitrogen (N) cycling, but their influence on nitrous oxide (N2O) emissions has not been quantitatively analyzed on a global scale. We conduct a comprehensive meta-analysis of 173 observations from 42 articles to evaluate global patterns of, and principal factors controlling, N2O emissions in the presence of root exudates and extracts. Overall, plant metabolites promoted soil N2O emissions by about 10%. However, the effects of plant metabolites on N2O emissions from soils varied with experimental conditions and properties of both metabolites and soils. Primary metabolites, such as sugars, amino acids, and organic acids, strongly stimulated soil N2O emissions, by an average of 79%, while secondary metabolites, such as phenolics, terpenoids, and flavonoids, often characterised as both biological nitrification inhibitors (BNIs) and biological denitrification inhibitors (BDIs), reduced soil N2O emissions by an average of 41%. The emission mitigation effects of BNIs/BDIs were closely associated with soil texture and pH, increasing with increasing soil clay content and soil pH on acidic and neutral soils, and with decreasing soil pH on alkaline soils. We furthermore present soil incubation experiments that show that three secondary metabolite types act as BNIs to reduce N2O emissions by 32-45% while three primary metabolite classes possess a stimulatory effect of 56-63%, confirming the results of the meta-analysis. Our results highlight the potential role and application range of specific secondary metabolites in bio-mitigation of global N2O emissions, and provide new biological parameters for N2O emission models that should help improve the accuracy of model predictions.

Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage

The dataset contains all the original raw files for the following study: Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage Marion Clavel1,2,*, Anita Bianchi1, Roksolana Kobylinska1, Roan Groh1,3, Juncai Ma4, Ranjith K. Papareddy1, Nenad Grujic1, Lorenzo Picchianti1,3, Ethan Stewart5, Michael Schutzbier1, Karel Stejskal1, Juan Carlos de la Concepcion1, Victor Sanchez de Medina Hernandez1,3, Yoav Voichek1, Pieter Clauw1, Joanna Gunis1, Gerhard Durnberger1, Jens Christian Muelders2,  Annett Grimm2, Arthur Sedivy5, Mathieu Erhardt6, Victoria Vyboishchikov1, Peng Gao1, Esther Lechner6, Emilie Vantard6, Jakub Jez5, Elisabeth Roitinger1, Pascal Genschik6, Byung-Ho Kang4, Yasin Dagdas1,*   Affiliations 1Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria. 2Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany 3Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria 4School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China 5Vienna Biocenter Core Facilities (VBCF), Vienna, Austria 6Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France   *Correspondence:           Marion Clavel (marion.clavel@mpimp-golm.mpg.de),                                         Yasin Dagdas (yasin.dagdas@gmi.oeaw.ac.at)   Abstract RNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response of Arabidopsis thaliana to three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response.  Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.   One archive corresponds to one main or supplemental figure.

Unraveling the local and regional determinants of the high plant diversity at marine rocky outcrops in Uruguay

This repository includes the data (environmental and species by plot) and codes associated to our work which analized the high plant diversity reported in Atlantic rocky outcrops of Uruguay.  In this study we analyzed the local determinants and regional processes that could determine this high plant diversity. Specifically, we evaluated the potential role of the regional species pool diversity (through the presence of different species assemblages according to their preferential environment or vegetation type), and the local determinants of plant diversity in the coast-inland gradient of stress and disturbance.

Species occurrence locations and environmental parameters used for predicting the potential planting regions of Pterocarpus santalinus

This study explores the habitat distribution of Pterocarpus santalinus, a valuable rosewood species, across China, focusing on its response to current and future climate changes. Utilizing the MaxEnt model, we assess its suitable habitat under present conditions and future climate scenarios (SSPs126, SSPs245, and SSPs585). Our findings reveal that the current suitable habitat, spanning approximately 409,600 km², is primarily located in the central and southern parts of Guangdong, Guangxi, Fujian, Yunnan, as well as in the Hainan provinces, along with the coastal regions of Taiwan, and the Sichuan-Chongqing border. The habitat's distribution is significantly influenced by climatic factors such as temperature seasonality (bio4), mean temperature of the wettest quarter (bio8), annual mean temperature (bio1), and annual precipitation (bio12), while terrain and soil factors play a lesser role. Under future climate scenarios, the suitable habitat for P. santalinus is projected to expand, with a northeastward shift in its distribution center. This research not only sheds light on the geoecological characteristics and geographical distribution of P. santalinus in China but also offers a scientific basis for planning its cultivation areas and enhancing cultivation efficiency under changing climate conditions.

The digital appendices for (2017) Robert Fortune - Plant Hunter From the Scottish Borders to the Pacific Rim in Search of Plants by David Kay Ferguson. ISBN: 9787566414519

At the back of the 2017 book "Robert Fortune - Plant Hunter From the Scottish Borders to the Pacific Rim in Search of Plants" by David Kay Ferguson. ISBN: 9787566414519 there is a CD with two files on it.  Notes & References. This is an archive of these Microsoft Word files. This archiving is done without the authors permission (I did try) and is intended to allow access to the data held within.

Study of the state of woody plants in arid conditions of Mangistau (Kazakhstan)

This study, conducted with meticulous attention to detail, comprehensively examines the state of plants and their adaptation to Kazakhstan's extra-arid climatic zone of the Mangistau. It uses the collections of woody plants from the Mangyshlak Experimental Botanical Garden in Aktau as a case study and extrapolates the results to the entire region. The study area is arid and unsuitable for many plants, so examining physiological adaptation mechanisms and strategies for preserving plants in unfavourable conditions is crucial. The study employed a range of methods, including the measurement of the intensity of transpiration, leaf hydration, and the content of chlorophyll A, B, and carotenoids. These methods were chosen for their proven effectiveness in similar studies and their ability to provide accurate and reliable data. The samples were also assessed using a point system for resistance to drought, phytophagy, gas tolerance, salt tolerance, winter hardiness, and soil fertility. The results obtained and entered into the IEBG platform “DinTseR” to assess the value of the introduction using a diagnostic scale revealed a high variability (up to 51.7-52.2%) of physiological indicators of growth and development. The highest values of transpiration intensity were observed in deciduous trees and shrubs, rose varieties (205-243 mg/g fresh leaf mass per hour), leaf water content - in climbing plants (68.9%), chlorophyll A and B content - in deciduous plants, and plants - old trees, fruit trees and varietal roses (3.46-3.93 and 1.34-1.84%). Their concentration in coniferous species is almost two times lower (0.63%). A correlation was also made between various significant factors. Twenty regression equations and forecasts have been identified that can be used to diagnose and assess resistance, thereby reducing the cost of determining the introduction value in the conditions of Mangistau. These findings are essential in understanding and preserving the unique flora of the Mangistau region.

opencc-by-4.0Jun 2023View details →

Results from, "Causal health impacts of power plant emission controls under modeled and uncertain physical process interference."

This repository contains results from the paper, "<a href="https://arxiv.org/abs/2306.05665">Causal health impacts of power plant emission controls under modeled and uncertain physical process interference</a>," by Wikle and Zigler (2024), to appear in Annals of Applied Statistics. The storage of these results helps facilitate access to and replication of the analysis in the paper. The results include output from the: <ol> <li>Sulfate analysis <ul> <li>tx-2016-100k-int-mx.RDS</li> </ul> </li> <li>Asthma analysis <ul> <li>asthma-pois-cut.RDS</li> <li>asthma-pois-plugin.RDS</li> <li>asthma-bart-cut.RDS</li> <li>asthma-bart-plugin.RDS</li> </ul> </li> <li>Medicare analysis <ul> <li>medicare-pois-cut.RDS</li> <li>medicare-pois-plugin.RDS</li> <li>medicare-bart-cut.RDS</li> <li>medicare-bart-plugin.RDS</li> </ul> </li> <li>Simulation study <ul> <li>simstudy-cm1-lm.RDS</li> <li>simstudy-cm1-bart.RDS</li> <li>simstudy-cm2-lm.RDS</li> <li>simstudy-cm2-bart.RDS</li> <li>simstudy-cm3-lm.RDS</li> <li>simstudy-cm3-bart.RDS</li> <li>simstudy-pm1-pois.RDS</li> <li>simstudy-pm1-bart.RDS</li> <li>simstudy-pm2-pois.RDS</li> <li>simstudy-pm2-bart.RDS</li> <li>simstudy-pm3-pois.RDS</li> <li>simstudy-pm3-bart.RDS</li> </ul> </li> <li>Log-linear BART sensitivity analysis <ul> <li>sensitivity-m100.RDS</li> <li>sensitivity-m200.RDS</li> <li>sensitivity-m300.RDS</li> <li>sensitivity-m400.RDS</li> <li>sensitivity-power05.RDS</li> <li>sensitivity-power1.RDS</li> <li>sensitivity-power15.RDS</li> <li>sensitivity-power2.RDS</li> <li>sensitivity-power25.RDS</li> <li>sensitivity-power3.RDS</li> <li>sensitivity-power4.RDS</li> <li>sensitivity-power5.RDS</li> </ul> </li> </ol> A description of these results can be found at <a href="https://github.com/nbwikle/estimating-interference">https://github.com/nbwikle/estimating-interference</a>, along with the R code used to generate these (and other results, such as figures) found in the manuscript and supplementary material.

Data from: Uncorrected soil water isotopes through cryogenic vacuum distillation may lead to a false estimation of plant water sources

Successful use of stable isotopes (δ2H and δ18O) in ecohydrological studies relies on the accurate extraction of unfractionated water from different types of soil samples. Cryogenic vacuum distillation (CVD) is a common laboratory-based technique used for soil water extraction; however, the reliability of this technique in reflecting soil water δ2H and δ18O is still of concern. This study examines the reliability of a newly developed automatic cryogenic vacuum distillation (ACVD) system through a set of pure water extraction. The impacts of extraction parameters (i.e., extraction time, temperature, and vacuum) and soil properties on the recovery of soil water δ2H and δ18O were further assessed for the ACVD and traditional extraction systems (TCVD) systems. Finally, the potential influences of the CVD technique on the prediction of plant water uptake were investigated through a sensitivity analysis. We demonstrated that the ACVD system was reliable for recovering the isotopic composition of pure water, with negligible biases of − 0.1 ± 0.3‰ for δ2H and 0.04 ± 0.09‰ for δ18O. Both ACVD and TCVD similarly extracted water from the rewetted soils when the extraction time of the ACVD system reached 240 min, but none of the CVD systems successfully recovered the isotopic signatures of doped water from soil materials. Mean δ2H offsets of extracted soil water were − 2.6 ± 1.3‰ and − 2.4 ± 1.7‰ for ACVD and TCVD, respectively; while mean δ18O offsets were − 0.16 ± 0.14‰ and − 0.39 ± 0.37‰. The isotopic offsets of CVD systems were positively correlated with soil clay content, and negatively correlated with soil water content. The use of corrected soil data (with CVD offsets) could improve the prediction of plant water uptake based on its high correlation with environmental factors. This study identifies the isotopic offsets of CVD systems (i.e., ACVD and TCVD) and provides possible solutions for better-predicting plant water sources. Even so, the wide use of CVD techniques probably induces noticeable uncertainties in predicting plant water uptake depths. The dataset of soil water extraction in this study will have implications for the technological development of CVD techniques.

Data and code from: Neighborhood habitat gains increase plant species richness in forest fragments - Rosenblad & Sullivan (2024)

This repository contains all data and R code necessary to reproduce the results of Rosenblad & Sullivan (2024) Neighborhood habitat gains increase plant species richness in forest fragments. README.md explains how the files fit together.

Effects of fire and invasive plants on tropical dry forest restorartion

The data collected is part of monitoring the ecological restoration process in a tropical dry forest. In this process, my research team conducted an experimental exercise, aiming to assess the natural regeneration around planted seedlings in burned sites compared to unburned sites. Additionally, we aimed to examine the effects of invasive species recruits and ruderal vegetation removal on seedlings and natural regeneration in both burned and unburned sites. For this research, we measured the planted seedlings and recorded the following data: height, weight, crown diameter, amount of radiation, and distance from the remaining forest edge. Furthermore, we counted the number of recruits, identified and searched for invasive potential in another database such as CABI. The planted seedlings were measured at two times; the first measurement was taken four months after planting, immediately after removing the ruderal vegetation around them. Forty-five days later, another round of ruderal vegetation removal in the plots was conducted, and after an additional 75 days, a final characterization of regeneration was performed

Data associated with studies on the following study: "Plant-level establishment can result from a single female Acanthococcus lagerstroemiae propagule"

These data are associated with the following study: "Plant-level establishment can result from a single female Acanthococcus lagerstroemiae propagule"

opencc-zeroDec 2023View details →

Data from: Dispersal-related plant traits are associated with range size in the Atlantic Forest

Aim: The efficiency of animal-mediated seed dispersal is threatened by declines of animal populations, especially in tropical forests. We hypothesise that large-seeded plants with animal-mediated dispersal tend to have limited geographic ranges and face an increased risk of extinction due to the potential decline in seed dispersal by large-bodied fruit-eating and seed-dispersing animals (frugivores) Location: Atlantic Forest, Brazil, South America Taxon: Angiosperms Methods: First, we collected dispersal-related trait (dispersal syndrome, fruit size, seed size), growth form (tree, climber, other) and preferred vegetation type (open, closed) data for 1,052 Atlantic Forest plant species. Next, we integrated these with occurrence records, extinction risk assessments, and phylogenetic trees. Finally, we performed phylogenetic generalized least squares (PGLS) regressions to test the direct and interactive effects of dispersal-related traits and vegetation type on geographical range size. Results: Large-seeded species had smaller range sizes than small-seeded species, but only for species with animal-mediated dispersal, not for those dispersed by abiotic mechanisms. However, plants with abiotic dispersal had overall smaller range sizes than plants with animal-mediated dispersal. Furthermore, we found that species restricted to forests had smaller ranges than those occurring in open or mixed vegetation. Finally, at least 29% of the Atlantic Forest flora is threatened by extinction, but this was not related to plant dispersal syndromes. Main Conclusions: Large-seeded plants with animal-mediated dispersal may be suffering from dispersal limitation, potentially due to past and ongoing defaunation of large-bodied frugivores, leading to small range sizes. Other factors, such as deforestation and fragmentation, will probably modulate such effects of dispersal on range size, and ultimately extinction. Our study sheds light on the relationship between plant traits, mutualistic interactions and distribution that are key to the functioning of tropical forests.

StArt Protocol for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.

StArt Protocol  for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.

Belowground plant competition: Uncoupling root response strategies of peas

Belowground plant competition was shown to induce varying responses, from increases to decreases in root biomass allocation or in directional root placement. Such inconsistencies could result from the fact that root allocation and directional growth were seldom studied together, even though they might represent different strategies. Moreover, variations in belowground responses might be due to different size hierarchies between plants, but this hypothesis was not studied previously. In a greenhouse rhizobox experiment, we examined the way both root allocation and directional root placement of Pisum sativum are affected by the size and density of Festuca glauca neighbors, and by nutrient distribution. We found that root allocation of P. sativum increased with the density and size of F. glauca. In contrast, directional root placement was unaffected by neighbor size and either increased toward or away from neighbors when nutrients were patchily or uniformly distributed, respectively. These results demonstrate that directional root placement under competition is contingent on the distribution of soil resources. Interestingly, our results suggest that root allocation and directional placement might be uncoupled strategies that simultaneously provide stress tolerance and spatial responsiveness to neighbors, thus highlighting the importance of measuring both when studying belowground plant competition.

opencc-by-4.0Dec 2023View details →

Plant community formation and species distribution pattern in relation to environmental variables in Endiras Natural Forest, northwest Ethiopia

The study was conducted in Endiras Forest, Northwest Ethiopia, so as to evaluate the effects of environmental variables on the patterns of plant community formation. A systematic random sampling technique was used to collect vegetation data from 56 (20 m x 20 m) plots laid at 100 m intervals on ten transects. In each plot, the species encountered and its percent cover abundance were recorded. The composite soil samples collected from 15 cm x 15 cm subplots were examined for 13 soil parameters. Communities were determined using cluster analysis. The Shannon-Wiener index was employed to quantify species diversity. The relationships between species and environmental variables were evaluated using CCA. Seventy three woody plant species, distributed in 38 families, were documented. Fabaceae was found to be the most species-rich family (21.9%). Five communities were generated from the cluster analysis. Nine environmental variables were found to be significant in determining patterns of community formation (Pr< 0.05). Organic matter, pH, and altitude are largely shaped the species distribution patterns. Various patterns of community formation demonstrate the need to design different conservation measures.

Data from: Widespread plant species temporal variation along environmental and microclimate gradients in Norwegian mountains

The effect of climate change on mountain vegetation is influenced by environmental factors and site effects. To monitor the effect of climate change we therefore need to understand species sensitivity to microclimate and environmental gradients. The objective of this study is to study widespread plant species temporal and spatial variation along environmental and microclimate gradients in Norwegian mountains along a coast-inland gradient. Occurrence and abundance of plant species were surveyed in 110 study plots in four mountains at two points in time, seven years apart. Of the 222 plant species registered, Salix herbacea, Phyllodoce caerulea, Carex bigelowii, Juncus trifidus, Vaccinium myrtillus, Avenella flexuosa, and Empetrum nigrum were widespread across all mountains. These species responded differently to environmental and microclimate gradients, and abundance data was more sensitive than occurrence data. During the short time span we observed some indications of response which might support the assumption that boreal species outcompete alpine species in the forest transition zone, but our data does not indicate this effect at higher altitudes. Monitoring of climate change in mountains need to include plots along environmental and microclimate gradients as well as abundance of a set of wide-spread plant species that represent both regional and local environmental and climate gradients. However, when monitoring perennial plant species, the necessity of long-time monitoring projects is high because such species develop slowly over several decades.