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440 results for “Potato”

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dryad36/100

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle ( Leptinotarsa decemlineata, Say)

Open the record for dataset details and reuse information.

publicJan 2021View details →

dryad36/100

High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

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publicSep 2025View details →

zenodo32/100

The effector secretome of the Irish potato famine pathogen Phytophthora infestans

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes. Haas et al. (2009) reported the sequence of the 240 megabases (Mb) genome of P. infestans. In this dataset we provide an annotated list of candidate effectors that we identified in the proteome of P. infestans T30-4 (Haas et al. 2009). We have frozen this list since 2015 and we reference all the effectors with “PITG_xxxxx” numbers from this list. The proteins can be cross-referenced to the GenBank sequences using these PITG_xxxxx numbers. The matching GenBank accession for the genome assembly is GCA_000142945.1. We also provide here the assembly and gtf files. Reference: <a href="https://kamounlab.dreamhosters.com/pdfs/Nature_09.pdf">Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.-H., Huitema, E., Jeong, D.-H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.</a>

opencc-by-4.0Dec 2019View details →

zenodo32/100

Contribution submitted by Antonella Garzelli for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

The European Food Safety Authority (EFSA) carried out a public consultation, from 27 February 2020 until 15 April 2020, to receive input from interested parties – organizations or private citizens - on a draft scientific opinion on the risks for animal and human health related to the presence of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products. The draft scientific opinion was prepared by the EFSA Panel on Contaminants in the Food Chain (CONTAM Panel), supported by the Working Group on Glycoalkaloids in feed and food. EFSA used the EU survey tool to receive comments on the draft scientific opinion, and the way these comments were considered for the finalisation of the opinion is described in the Technical Report available at: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2F10.2903%2Fsp.efsa.2020.EN-1905&data=02%7C01%7C%7C242adcee21744b01890408d82cba24b4%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637308525272584775&sdata=97Tc3%2FrT1SXtzIN14PCCvUv0OYyaiSO1H76iezwqvnQ%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2020.EN-1905</a>. Some contributors also attached files to the comments submitted via the EU survey tool. For transparency reasons these files are made available in the public domain as Zenodo uploads.

opencc-by-4.0Aug 2020View details →

zenodo32/100

Contribution submitted by STARCH EU for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

opencc-by-4.0Aug 2020View details →

zenodo32/100

Contribution submitted by Matthew Walker for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

opencc-by-4.0Aug 2020View details →

dryad32/100

Construction of a chromosome-scale long-read reference genome assembly for potato

Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. Findings: Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared to the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the numbersof contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions: Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

opencc-zeroAug 2020View details →

dryad32/100

DNA methylation and phenotypic data from: Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

DNA methylation can be environmentally modulated and play a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) was assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability were positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.

opencc-zeroAug 2020View details →

zenodo32/100

PLATE 1 in Empoasca fabalis (Hemiptera: Cicadellidae): first report of an invasive pest of sweet potatoes in Portugal (Madeira Island)

PLATE 1. Female of Empoasca fabalis (A). Fore wing venation of Empoascini of Madeira: E. fabalis (B); E. alsiosa (C); A. decedens (D); Morphotype A (E); Morphotype B (F); Morphotype C (G). Damage caused by E. fabalis to the leaves of sweet potatoes (H, I).

opennotspecifiedAug 2020View details →

zenodo32/100

Aphicidal and antifeedant activity of Synandrospadix vermitoxicus extracts against Myzus persicae on potato plants

Supplemental raw data and statistics of López-Isasmendi et al.

opencc-by-4.0Jan 2021View details →

dryad32/100

Data from: Suppression of reproductive characteristics of the invasive plant Mikania micrantha by sweet potato competition

Background: As a means of biologically controlling Mikania micrantha H.B.K. in Yunnan, China, the influence of sweet potato [Ipomoea batatas (L.) Lam.] on its reproductive characteristics was studied. The trial utilized a de Wit replacement series incorporating six ratios of sweet potato and M. micrantha plants in 25 m2 plots over two years. Results: Budding of M. micrantha occurred at the end of September; flowering and fruiting occurred from October to February. Flowering phenology of M. micrantha was delayed (P<0.05), duration of flowering and fruiting was reduced (P<0.05) and duration of bud formation was increased (P<0.05) with increasing proportions of sweet potato. Reproductive allocation, reproductive investment and reproductive index of M. micrantha were significantly reduced (P<0.05) with increasing sweet potato densities. Apidae bees, and Calliphoridae or Syrphidae flies were the most abundant visitors to M. micrantha flowers. Overall flower visits decreased (P<0.05) as sweet potato increased. Thus the mechanism by which sweet potato suppressed sexual reproduction in M. micrantha was essentially two-fold: causing a delay in flowering phenology and reducing pollinator visits. The number, biomass, length, set rate, germination rate, and 1000-grain dry weight of M. micrantha seeds were suppressed (P<0.05) by sweet potato competition. With proportional increases in sweet potato, sexual and asexual seedling populations of M. micrantha were significantly reduced (P<0.05). The mortality of both seedling types increased (P<0.05) with proportional increases in sweet potato. Conclusions: These results suggest that sweet potato significantly suppresses the reproductive ability of the invasive species M. micrantha, and is a promising alternative to traditional biological control and other methods of control. Planting sweet potato in conjunction with other control methods could provide a comprehensive strategy for managing M. micrantha. The scenario of controlling M. micrantha by utilizing a crop with a similar growth form may provide a useful model for similar management strategies in other systems.

opencc-zeroDec 2015View details →

dryad32/100

Data from: Rapid adaptation of the Irish potato famine pathogen Phytophthora infestans to changing temperature

Temperature plays a multidimensional role in host-pathogen interactions. As an important element of climate change, elevated world temperature resulting from global warming presents new challenges to sustainable disease management. Knowledge of pathogen adaptation to global warming is needed to predict future disease epidemiology and formulate mitigating strategies. In this study, 21 Phytophthora infestans isolates originating from seven thermal environments were acclimated for 200 days under stepwise increase or decrease of experimental temperatures and evolutionary responses of the isolates to the thermal changes were evaluated. We found temperature acclimation significantly increased the fitness and genetic adaptation of P. infestans isolates at both low and high temperatures. Low temperature acclimation enforced the counter-gradient adaptation of the pathogen to its past selection and enhanced the positive association between the pathogen's intrinsic growth rate and aggressiveness. At high temperatures we found that pathogen growth collapsed near the maximum temperature for growth, suggesting a thermal niche boundary may exist in the evolutionary adaptation of P. infestans. These results indicate that pathogens can quickly adapt to temperature shifts in global warming. If this is associated with environmental conditions favouring pathogen spread it will threaten future food security and human health and require the establishment of mitigating actions.

opencc-zeroNov 2019View details →

dryad32/100

Data from: Costs and tradeoffs of resistance and tolerance to belowground herbivory in potato

1. The success of sustainable crop production depends on our ability to select or create varieties that can allocate resources to both growth and defence. However, breeding efforts have emphasized increases in yields but have partially neglected defence traits against pests. Estimating the costs of multiple defences against tuber herbivores and the tradeoffs among them, as well as understanding the relationship between yield and multiple defences is still unknown but relevant to both basic and applied ecology. 2. Using twenty commercial potato varieties available in Colombia and the tuber herbivore Tecia solanivora, we tested whether high yielding varieties show a reduction in three types of defence: constitutive and induced resistance, as well as tolerance. Specifically, we determined (1) the costs in terms of yield of all three defences, (2) the possible tradeoffs among them, and (3) if oviposition preference was related to the expression of these defences. 3. We detected no costs in terms of yield of constitutive and induced resistance to tuber damage. We did, however, find evidence of costs of being able to tolerate tuber herbivory. While we found no tradeoffs among any of the estimated defences, there was a positive correlation between aboveground compensatory growth and tolerance in terms of tuber production, suggesting that after damage there are no shifts in the allocation of resources from aboveground to belowground biomass. Finally, we found that females laid more eggs on those varieties with the lowest level of constitutive resistance. 4. Synthesis and applications. Our findings suggest that in potatoes, breeding for higher yields has not caused any reduction in constitutive or induced resistance to tuber damage. This is not the case for tolerance where those varieties with higher yields are also less likely to tolerate tuber damage. Given the high incidence of tuber pests in Colombia, selecting for higher tolerance could allow for high productivity in the presence of herbivores. Finding mechanisms to decouple the tolerance response from yield should be a new priority in potato breeding in Colombia to guarantee a higher yield in both the presence and absence of herbivores.

opencc-zeroDec 2016View details →

dryad32/100

Data from: Tailored flower strips promote natural enemy biodiversity and pest control in potato crops

1. Sown flower strips are increasingly implemented within agri-environment schemes (AES) to increase functional biodiversity and ecosystem services such as pollination or natural pest control, but their effectiveness in achieving these goals remains poorly studied. 2. We tested the performance of experimentally sown annual flower strips specifically designed to promote natural enemies of aphids and their pest control services (tailored flower strips) in adjacent potato crops (n=8) compared to control fields (n=10). Flower strips consisted of 11 plant species providing abundant floral and extra-floral resources. 3. The abundance of key natural enemies of aphids (hoverflies, lacewings and ladybirds) and hoverfly species richness was greatly enhanced in tailored flower strips compared to potato control strips. This resulted in an average increase in the number of eggs deposited by hoverflies and lacewings by 127 % and 48 %, respectively, and a reduction in the number of aphids by 75 % in adjacent potato crops. 4. Synthesis and applications. We conclude that tailored flower strips can be an effective agri-environmental measure to enhance natural enemies and aphid control in nearby crops. Indeed, tailored flower strips may help to reduce insecticide input in potato production as they significantly decrease the probability that action thresholds are reached. Promoting natural enemy abundance and diversity, as observed for hoverflies, may increase the stability of pest control and provide additional benefits to agro-ecosystems in terms of natural enemy conservation. We thus recommend establishing tailored flower strips as a promising management option to reconcile the objectives of ecological intensification and biodiversity conservation.

opencc-zeroDec 2015View details →

dryad32/100

Data from: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans

The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in recent decades. Recently, complete P. infestans mitogenome sequences from 19th-century herbarium specimens were shown to belong to a unique lineage (HERB-1) predicted to be rare or extinct in modern times. We report 44 additional P. infestans mitogenomes: four from 19th-century Europe, three from 1950s U.K. and 34 from modern populations across the New World. We use phylogenetic analyses to identify the HERB-1 lineage in modern populations from both Mexico and South America, and to demonstrate distinct mitochondrial haplotypes were present in 19th-century Europe, with this lineage initially diversifying 75 years before the first reports of potato late blight.

opencc-zeroDec 2013View details →

dryad32/100

Data from: High levels of diversity and population structure in the potato late blight pathogen at the Mexico center of origin

Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their center of origin, and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the center of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, have focused on the Toluca Valley, whereas neighboring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala, and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala, and population subdivision that was strongly associated with geographical region. We determined that population structure in Central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in Central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the U.S. and elsewhere.

opencc-zeroDec 2015View details →

dryad32/100

Data from: Conquering the inner couch potato: precommitment is an effective strategy to enhance motivation for effortful actions

Letting effort-free gratification derail us from effort-requiring goals is one reason why we fail to realize health-relevant intentions like 'exercise regularly'. We tested the effectiveness of the self-control strategy precommitment in such effort-related conflicts, using a novel laboratory choice paradigm, where participants could precommit to an effort-requiring large reward by pre-eliminating an effort-free small reward from their choice set. Our participants used precommitment frequently and effectively, such that they reached effort-requiring large rewards more often. Using computational modelling and Bayesian model comparisons, we assessed whether participants employed precommitment to avoid anticipated willpower failures (i.e. as a self-regulatory measure) or to maximize their motivation to choose the effort-requiring option (i.e. as a self-motivational measure). Observed choices and precommitment decisions were consistent with the motivation maximization hypothesis, but not the willpower hypothesis. Our findings show that offering precommitment is effective in helping individuals optimize their motivation and choice behaviour and thereby achieve effort-requiring goals, and strongly encourage application of precommitment schemes in exercise and rehabilitation interventions. This article is part of the theme issue 'Risk taking and impulsive behaviour: fundamental discoveries, theoretical perspectives and clinical implications'.

opencc-zeroDec 2018View details →

dryad32/100

Data from: Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces

We analyzed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America super-region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kind of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Meso-America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of germplasm collections.

opencc-zeroDec 2010View details →

dryad32/100

Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.

opencc-zeroDec 2016View details →

dryad32/100

Data from: On the origin of sweet potato (Ipomoea batatas (L.) Lam) genetic diversity in New Guinea, a secondary centre of diversity

New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.

opencc-zeroDec 2012View details →

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Allen Brain Atlas

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allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record