Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,710
datasets available to search
ShareScore release 0.7.1
Dataset results
1,710 results for “medicago”
Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions
<p><em>Medicago</em> <em>truncatula</em> is a model legume that has been extensively investigated in diverse subdisciplines of plant science. <em>Medicago</em> <em>littoralis</em> can interbreed with <em>M</em>. <em>truncatula</em> and <em>M</em>. <em>italica</em>; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that <em>M</em>. <em>truncatula</em> accessions are heterogeneous, but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse <em>M</em>. <em>truncatula</em> accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both <em>M</em>. <em>truncatula</em> and <em>M</em>. <em>littoralis</em>. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a <em>M</em>. <em>italica</em> subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the <em>M</em>. <em>littoralis</em> subclade. Our results suggest that the <em>M</em>. <em>truncatula</em> accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.</p>
Insights into species delimitation of selected species in the flowering plant genus Medicago section Buceras (Leguminosae)
<p>The genus <em>Medicago</em> (Leguminosae, Papilionoideae) contains about 90 species including the important forage crop alfalfa <em>Medicago sativa</em> and the genomic model <em>Medicago truncatula</em>. Despite intensive research on the genus because of its agricultural importance, there is a relative lack of information about chromosome number and genome size in some <em>Medicago</em> species, especially those from section <em>Buceras</em> that were formerly placed in the sister genus <em>Trigonella</em>, and are paraphyletic to the remainder of the genus <em>Medicago</em>. Past studies revealed that previous species delimitations did not conform well with complex patterns of morphological or genetic variation. Some published chromosome numbers, e.g., 2n = 28 and 2n = 44, differ from those of the rest of the genus, which are mostly 2n = 16 or polyploids thereof, although some cases of aneuploid reduction or dysploidy (e.g., 2n = 14) do exist. Here we estimated phylogenetic relationships of 42 accessions corresponding to 14 currently recognized <em>Medicago</em> species that are paraphyletic to the remainder of <em>Medicago</em> with a focus on <em>Medicago monantha</em>; for a number of those accessions, we obtained estimates of genome size (39) and chromosome number (14). We can confirm the delimitation of two species within section <em>Buceras</em>, and our data suggest that there are at least two entities with distinct geographic distributions within the currently recognized species <em>M. monantha,</em> which differ in chromosome number and genome size. Our data also suggest that polyploidy and post-polyploid descending dysploidy played a significant role in genome evolution within section <em>Buceras.</em> Our data provide a strong foundation for whole-genome sequencing projects and further in-depth research of these paraphyletic lineages.</p>
Niche conservatism limits the distribution of Medicago in the tropics
Open the record for dataset details and reuse information.
Data from: Rapid establishment of a flowering cline in Medicago polymorpha after invasion of North America
Open the record for dataset details and reuse information.
Insights into species delimitation of selected species in the flowering plant genus Medicago section Buceras (Leguminosae)
Open the record for dataset details and reuse information.
A public mid-density genotyping platform for alfalfa (Medicago sativa L.)
Open the record for dataset details and reuse information.
Aphid infestation differently affects the defences of nitrate-fed and nitrogenfixing Medicago truncatula and alters symbiotic nitrogen fixation
Open the record for dataset details and reuse information.
Alfalfa (Medicago sativa) salt tolerance/mutualistic bacteria inoculation
Open the record for dataset details and reuse information.
Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions
Open the record for dataset details and reuse information.
Data from: Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes
Open the record for dataset details and reuse information.
Kellogg Biological Station site, station Treatment 3, organic-based low chemical input (banded herbicide, starter N), winter leguminous crop, annual tillage and post-planting cultivation, study of aboveground net primary productivity of Medicago sativa in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago sativa measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Kellogg Biological Station site, station Treatment 4, certified oganic, no chemical inputs, annual tillage, rotary-hoed to control weeds, study of aboveground net primary productivity of Medicago sativa in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago sativa measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Kellogg Biological Station site, station Treatment 7, native successional treatment, abandoned after spring plowing in 1989, study of aboveground net primary productivity of Medicago lupulina in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago lupulina measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Kellogg Biological Station site, station Treatment SF, old field successional community, never tilled, study of aboveground net primary productivity of Medicago lupulina in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago lupulina measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Kellogg Biological Station site, station Kellogg Biological Station, study of aboveground net primary productivity of Medicago lupulina in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago lupulina measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Kellogg Biological Station site, station Kellogg Biological Station, study of aboveground net primary productivity of Medicago sativa in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Medicago sativa measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Data from: Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea
Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. RADseq has been a popular sequencing technique for the reconstruction of hybridization in the Next Generation Sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization but the specific hybrid origins of taxa have not been yet clarified. Methods: We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex hybridization patterns. Results: Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while less clear signals were observed for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata and M. sativa. Conclusions: Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when most divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.
Data from: Rapid evolution of Medicago polymorpha during invasion shifts interactions with the Soybean looper
The Enemy Release Hypothesis posits that invasion of novel habitats can be facilitated by the absence of coevolved herbivores. However, a new environment and interactions with unfamiliar herbivores may impose selection on invading plants for traits that reduce their attractiveness to herbivores or for enhanced defenses compared to native host plants, leading to a pattern similar to Enemy Release but driven by evolutionary change rather than ecological differences. The Shifting Defense Hypothesis posits that plants in novel habitats will shift from specialized defense mechanisms to defense mechanisms effective against generalist herbivores in the new range. We tested these ideas by comparing herbivore preference and performance of native (Eurasia) and invasive (New World) range Medicago polymorpha , using a generalist herbivore, the soybean looper, that co-occurs with M. polymorpha in its New World invaded range. We found that soybean loopers varied in preference and performance depending on host genotype and that overall the herbivore preferred to consume plant genotypes from naïve populations from Eurasia. This potentially suggests that range expansion of M. polymorpha into the New World has led to rapid evolution of a variety of traits that have helped multiple populations become established, including those that may allow invasive populations to resist herbivory. Thus, enemy release in a novel range can occur through rapid evolution by the plant during invasion, as predicted by the Shifting Defense Hypothesis, rather than via historical divergence.
Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. Results: In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. Conclusions: The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.