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opencc-by-4.0Feb 2023View details →

Phenotypic variations of primary metabolites yield during alcoholic fermentation in the Saccharomyces cerevisiae species

Supplementary data including the data set used for the" Phenotypic variations of primary metabolites yield during alcoholic fermentation in the Saccharomyces cerevisiae species" publication.   Abstract: Saccharomyces cerevisiae, as the workhorse of alcoholic fermentation, is a major actor of winemaking. In this context, this yeast species performs alcoholic fermentation to convert sugars from the grape must into ethanol and CO2 with an outstanding efficiency: it reaches on average 92% of the maximum theoretical yield of conversion. Primary metabolites produced during fermentation stand for a great importance in wine where they significantly impact wine characteristics. Ethanol indeed does, but others too, which are found in lower concentrations: glycerol, succinate, acetate, ⍺-ketoglutarate… Their production, which can be characterised by a yield according to the amount of sugars consumed, is known to differ from one strain to another. S. cerevisiae is known for its great genetic diversity and plasticity that is directly related to its living environment, natural or technological and therefore to domestication. This leads to a great phenotypic diversity of metabolites production. However, the range of metabolic diversity is variable and depends on the pathway considered. In the aim to improve wine quality, the selection, development and use of strains with dedicated metabolites production without genetic modifications can rely on the natural diversity that already exists. Here we detail a screening that aims to assess this diversity of primary metabolites production in a set of 51 S. cerevisiae strains from various genetic backgrounds (wine, flor, rum, West African, sake…). To approach winemaking conditions, we used a synthetic grape must as fermentation medium and measured by HPLC five main metabolites. Results obtained pointed out great yield differences between strains and that variability is dependent on the metabolite considered. Ethanol appears as the one with the smallest variation among our set of strains, despite it’s by far the most produced. A clear negative correlation between ethanol and glycerol yields has been observed, confirming glycerol synthesis as a good lever to impact ethanol yield. Genetic groups have been identified as linked to high production of specific metabolites, like succinate for rum strains or alpha-ketoglutarate for wine strains. This study thus helps to define the phenotypic diversity of S. cerevisiae in a wine-like context and supports the use of ways of development of new strains exploiting natural diversity. Finally, it provides a detailed data set usable to study diversity of primary metabolites production, including common commercial wine strains.

Data for: Phenotypic plasticity increases exposure to extreme climatic events that reduce individual fitness

Climate models, and empirical observations, suggest that anthropogenic climate change is leading to changes in the occurrence and severity of extreme climatic events (ECEs). Effects of changes in mean climate on phenology, movement, and demography in animal and plant populations are well documented. In contrast, work exploring the impacts of ECEs on natural populations is less common, at least partially due to the challenges of obtaining sufficient data to study such rare events. Here, we assess the effect of changes in ECE patterns in a long-term study of great tits, near Oxford, over a 56-year period between 1965 and 2020. We document marked changes in the frequency of temperature ECEs, with cold ECEs being twice as frequent in the 1960s than at present, and hot ECEs being ~three times more frequent between 2010 and 2020 than in the 1960s. While the effect of single ECEs was generally quite small, we show that increased exposure to ECEs often reduces reproductive output, and that in some cases, the effect of different types of ECE is synergistic. We further show that long-term temporal changes in phenology, resulting from phenotypic plasticity, lead to an elevated risk of exposure to low-temperature ECEs early in reproduction, and hence suggest that changes in ECE exposure may act as a cost of plasticity. Overall, our analyses reveal a complex set of risks of exposure and effects as ECE patterns change and highlight the importance of considering responses to changes in both mean climate and extreme events. Patterns in exposure and effects of ECEs on natural populations remain underexplored and continued work will be vital to establish the impacts of ECEs on populations in a changing climate.

opencc-by-4.0Mar 2023View details →

Supplemental material for the paper "Genotype-phenotype correlation, clinical presentation, and feminizing surgery in children with congenital adrenal hyperplasia - a nationwide study"

This dataset provides documentation for the translation between historical nomenclature for variants in the CYP21A2 gene to the Human genome variation society nomenclature.  Furthermore, it provides data on all Danish CYP21A2 variants included in the study and the translation into genotype groups: Null, A, B, C, and D.

Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses

Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop in the USA. It is a native, perennial, warm-season grass, and has broad adaptability. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Significant genetic variation for biomass yield observed in lowland switchgrass hybrids. Due to the quantitative inheritance of biomass yield, varietal improvement for the trait through conventional breeding is slow. Therefore, quantitative trait loci (QTL) mapping is used to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped seven biparental crosses and one combined cross of two biparental crosses (30 to 96 F1s) between lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass yield, plant height, and clonal mass scores in a simulated-sward plot with two replications at two locations in Tennessee from 2019 to 2021. The crosses were genotyped using 17,251 single nucleotide polymorphisms generated through genotyping-by-sequencing. QTL mapping was performed using a single-QTL model in R-QTL. The study identified major QTL for biomass yield, plant height, and clonal mass scores resided on chromosomes 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively. The dataset contains five files describing the phenotype and genotype of each individual used in the quantitative trait loci (QTL) analysis. <ul> <li>'File 1' contains biomass yield, plant height, and clonal mass data for each genotype and parents evaluated at two locations in Tennessee; the Plateau Research and Education Center (PREC), Crossville and East Tennessee Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant height and biomass yield were measured at maturity, and clonal mass scores were evaluated after harvesting biomass.</li> <li>'File 2' has the genotype name, library, index, total reads, bases, and the Phred quality score (Q30). Young leaf tissue was collected from each F1 progeny and parent, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) procedure. The extracted DNA was genotyped at the USDA-ARS Western Regional Research Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was performed on 951 lines (F1s and their parents) using the PstI-MspI GBS protocol. The quality of these sequences showed that 94.4% of the bases were at or above Q30. Reads were mapped to version 5.0 of the switchgrass reference genome. Single nucleotide polymorphism (SNP) calling was performed, and redundant markers were filtered out for linkage map construction. 'File 3' has SNP ID numbers, SNP locations on chromosomes, map positions, and SNP scores. The cross was used as a four-way cross for QTL analysis, where the male parent Kanlow (K) was assigned as '1', and the female parent Alamo (A) was assigned as '2'.</li> <li>The phased output data from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC, BC, AD, and BD, respectively ('File 3').</li> <li>The progeny file ('File 4') contains the name of the parents used for making crosses and their progenies.</li> <li>A consensus linkage map ('File 5') was produced with Lep-Map3 software. The linkage map contains 18 linkage groups associated with 18 switchgrass chromosomes, marker size (bp), map position (cM) based on male and female maps, and map order.</li> </ul>

opencc-by-4.0May 2020View details →

Transgenerational phenotypic plasticity of diapause induction and related fitness cost in a commercial strain of the parasitoid Aphidius ervi Haliday

Dataset. Diapause is an adaptation that insects have evolved to synchronize their life cycle with that of seasonal climatic changes and resources availability. However, cues for its induction are not always clear and, in some cases, a maternal effect may be involved. At the population level, just a part of the individuals may exhibit diapause with important consequences in terms of winter survival. Moreover, clear indicators of diapause state are difficult to identify. Diapause induction was thus investigated in the aphid parasitoid species Aphidius ervi Haliday (Hymenoptera: Braconidae) developing in the aphid Sitobion avenae (Hemiptera: Aphididae) at four crossed photothermal regimes (16 °C and 8 °C, 16:8 h L:D and 8:16 h L:D), and during 2 successive generations. We analyzed the reliability of changes in mummy color to assess for the diapausing state compared to dissections, and we measured parasitoid morphological and physiological traits. We observed that the proportion of dark brown mummies increased after one generation under low photothermal regime compared to other regimes. No diapause was recorded at 16 °C, 16:8 h L:D, while we observed 16.2% and 67.5% diapause incidence at 8 °C, 8:16 h L:D, at 1st and 2nd generation, respectively. Diapause induction is thus increased by short day-length conditions and low temperatures as well as by maternal effects. All parasitoid life-history traits (weight, size, fat content, water content, egg-load, and longevity) were affected by the photothermal regime and/or the generation. These results raise new questions on the environmental thresholds needed to induce diapause and on survival and adaptation potential of commercially available parasitoid strains in different environments.

Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

Animal feces from livestock farming can be a major source of antibiotic resistance to the environment, but a clear gap exists on how the resistance reservoir in feces alters as farming activities intensify. Here, we sampled feces from eight Chinese farms, where yak, sheep, pig, and horse were reared under free-range to intensive conditions, and determined fecal resistance using both genotype and phenotype approaches. Animals reared intensively exhibited increased diversity of antibiotic resistance genes (ARGs) and greater resistance phenotypes in feces, which were cross-correlated. Furthermore, at the metagenome contig level, ARGs were co-located with mobile genetic elements at a higher frequency (27.38%) as farming intensified, with associated resistance phenotypes being less coupled with bacterial phylogeny. Intensified farming also expanded the multidrug resistance preferentially carried on pathogens in fecal microbiomes. Overall, farming intensification can increase antibiotic resistance genotypes and phenotypes in domestic animal feces, with implications for environmental health.

Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly

Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly Bicyclus dorothea originating from rainforest and ecotone habitats in Cameroon under common garden conditions. We also sampled wild-caught butterflies from forest and ecotone sites and used RADseq to explore genome-wide population differentiation. We found differences in the level of phenotypic plasticity across habitats. Specifically, ecotone populations exhibited greater sensitivity in wing eyespot features with variable development temperatures relative to rainforest populations. Known adaptive roles of wing eyespots in Bicyclus species suggest that this morphological plasticity is likely under divergent selection across environmental gradients. However, we found no distinct population structure of genome-wide variation between habitats, suggesting high levels of ongoing gene flow between habitats is homogenizing most parts of the genome.

openother-openApr 2023View details →

Database for "Phenotype-fitness relationships and pollen transfer efficiency of five orchid species with different pollination strategies" American Journal of Botany 2023

Public data from the paper: Phenotype-fitness relationships and pollen transfer efficiency of five orchid species with different pollination strategies by M. Capò, J. Borràs, S. Perellò-Suau, J. Rita and J. Cursach, published in American Journal of Botany 2023. <a href="https://doi.org/10.5281/zenodo.7826601">DOI: 10.5281/zenodo.7826601</a>

opencc-zeroApr 2023View details →

Data for: Defining the relationship between phylogeny, clinical manifestation and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations

This study looked for correlations between molecular identification, clinical manifestation and morphology for Trichophyton interdigitale and T. mentagrophytes. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Micro- and macromorphology and physiology were analysed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/scored phenotypic features, statistically significant differences between species were found only in growth rates at 37°C and in the production of spiral hyphae but none of these features was diagnostic. Correlations were found between T. interdigitale and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis. The MLST approach showed that ITS genotyping of T. mentagrophytes isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species' names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical manifestations and sources of infections, which keep those names alive. This practice is questionable because the use of both names confuses identification, leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as MALDI-TOF MS fail to distinguish these species. To avoid further confusion and simplify identification in practice, we recommend using the name T. mentagrophytes for the entire complex. When clear differentiation of populations corresponding to T. interdigitale and T. indotineae is possible based on molecular data, we recommend optionally using a variety rank: T. mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.

opencc-zeroApr 2023View details →

A metadata framework for electronic phenotypes

As many phenotyping algorithms are being created to support precision medicine or observational studies using electronic patient data, it is getting increasingly difficult to identify the right algorithm for the right task. A metadata framework promises to help curate phenotyping algorithms to facilitate more efficient and accurate retrieval. We recruited 20 researchers from two phenotyping communities, the eMERGE and the OHDSI communities, and used a mixed-methods approach to develop the metadata framework. Once we achieved a consensus of 39 metadata elements, we surveyed 47 new researchers from these communities to evaluate the utility of the metadata framework. Two researchers were also asked to use it to annotate eight type 2 diabetes mellitus phenotypes. The survey consisted of a series of multiple-choice questions, which allowed rating of the utility of each element on a scale of 1-5, and open-ended questions, which allowed for narrative responses. More than 90% of respondents rated metadata elements concerning phenotype definition and validation methods and metrics with a score of 4 or 5. Our thematic analysis of the respondents' feedback indicates that the strengths of the metadata framework were its ability to capture rich descriptions, explicitness, compliance with data standards, comprehensiveness in validation metrics, and ability to enable cross-phenotype searches. Limitations were its complexity for data collection and entailed costs.

opencc-zeroMay 2023View details →

Parental care results in a greater mutation load, for which it is also a phenotypic antidote

Benevolent social behaviours, such as parental care, are predicted to relax selection against deleterious mutations, enabling them to persist. We tested this prediction experimentally using burying beetles, Nicrophorus vespilloides, which make an edible nest for their larvae, whom they nourish and defend. For 20 generations, we allowed replicate experimental burying beetle populations to evolve either with post-hatching care ('Full Care' populations) or without it ('No Care' populations). Lineages were seeded from these experimental populations and then inbred to expose differences in their mutation load. Outbred lineages served as controls. Half the lineages received post-hatching care, half did not. We found that inbred lineages derived from the Full Care populations had lower breeding success and went extinct more quickly than lineages derived from the No Care populations – but only when offspring received no post-hatching care. We infer that Full Care lineages carried more recessive deleterious mutations. When parents provided care, the developmental environment was sufficiently benign that broods had higher survival, whether the population had a high mutation load or not. We suggest that the increased mutation load caused by parental care increases a population's dependence upon care. This could explain why care is seldom lost once it has evolved.

opencc-zeroMay 2023View details →

The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus

Wild animals are under constant threat from a wide range of micro- and macroparasites in their environment. Animals make immune responses against parasites, and these are important in affecting the dynamics of parasite populations. Individual animals vary in their anti-parasite immune responses. Genetic polymorphism of immune-related loci contributes to inter-individual differences in immune responses, but most of what we know in this regard comes from studies of humans or laboratory animals; there are very few such studies of wild animals naturally infected with parasites. Here we have investigated the effect of Single Nucleotide Polymorphisms (SNPs) in immune-related loci (the MHC, and loci coding for cytokines and Toll-like receptors) on a wide range of immune and infection phenotypes in UK wild house mice, Mus musculus domesticus. We found strong associations between SNPs in various MHC and cytokine-coding loci on both immune measures (antibody concentration and cytokine production) and on infection phenotypes (infection with mites, worms and viruses). Our study provides a comprehensive view of how polymorphism of immune-related loci affects immune and infection phenotypes in naturally infected wild rodent populations.

opencc-zeroMay 2023View details →

Data from: Phenotypic clines in herbivore resistance and reproductive traits in wild plants along an agricultural gradient

The conversion of natural landscapes to agriculture is a leading cause of biodiversity loss worldwide. While many studies examine how landscape modification affects species diversity, a trait-based approach can provide new insights into species responses to environmental change. Wild plants persisting in heavily modified landscapes provide a unique opportunity to examine species' responses to land use change. Trait expression within a community plays an important role in structuring species interactions, highlighting the potential implications of landscape mediated trait changes on ecosystem functioning. Here we test the effect of increasing agricultural landscape modification on defensive and reproductive traits in three commonly occurring Brassicaceae species to evaluate plant responses to landscape change. We collected seeds from populations at spatially separated sites with variation in surrounding agricultural land cover and grew them in a greenhouse common garden, measuring defensive traits through an herbivore no-choice bioassay as well as reproductive traits such as flower size and seed set. In two of the three species, plants originating from agriculturally dominant landscapes expressed a consistent reduction in flower size and herbivore leaf consumption. One species also showed reduced fitness associated with increasingly agricultural landscapes. These findings suggest that wild plants are responding to landscape modification, highlighting that species diversity alone does not fully capture the effects of land use change.

opencc-zeroJun 2023View details →

What happens when the lights are left on? Transcriptomic and phenotypic habituation to light pollution

Artificial light at night (ALAN) is one of the most ubiquitous human-induced environmental stressors. ALAN can induce immediate behavioral and physiological changes in animals, sometimes leading to severe health consequences. Nevertheless, many organisms persist in light-polluted environments and may have mechanisms of habituating to ALAN, reducing responses to repeated exposure over time. The capacity for animals to habituate to ALAN has yet to be tested experimentally. We conducted a 6-month repeated-measures experiment with zebra finches (Taeniopygia guttata) to test whether birds can habituate to repeated ALAN exposure. We measured individual changes in behavior, physiology (oxidative stress and telomere attrition), and gene expression to test for concordance among behavioral, physiological, and transcriptomic responses to ALAN. We present evidence of tolerance to chronic ALAN exposure, persistent behavioral responses lasting 8 weeks post-exposure, and habituation to subsequent re-exposure. We found no changes in telomere attrition and a decrease in oxidative stress associated with ALAN exposure, indicating potential protective effects of long-term dim ALAN. Changes in blood transcriptome within individuals revealed unique responses to both previous ALAN exposure and subsequent re-exposure. These results represent organismal resilience to chronic stressors and shed light on the capacity of individuals to persist in an increasingly light-polluted world.

opencc-zeroJun 2023View details →

Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition

Pigs infected with Salmonella may excrete large amounts of Salmonella, increasing the risk of spread of this pathogen in the food chain. Identifying Salmonella high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with Salmonella. Immune response was studied through total blood cell counts, production of anti-Salmonella antibodies and cytokines, and gene expression quantification. Total Salmonella shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with Salmonella induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to Salmonella modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing Salmonella high shedding in livestock.

opencc-zeroJun 2023View details →

Similar transcriptomic responses to early and late drought stresses produce divergent phenotypes in sunflower (Helianthus annuus L.)

Cultivated sunflower (Helianthus annuus L.) exhibits numerous phenotypic and transcriptomic responses to drought. However, the ways in which these responses vary with differences in drought timing and severity are insufficiently understood. We used phenotypic and transcriptomic data to evaluate the response of sunflower to drought scenarios of different timing and severity in a common garden experiment. Using a semi-automated outdoor high-throughput phenotyping platform, we grew six oilseed sunflower lines under control and drought conditions. Our results reveal that similar transcriptomic responses can have disparate phenotypic effects when triggered at different developmental time points. Leaf transcriptomic responses, however, share similarities despite timing and severity differences (e.g., 523 differentially expressed genes (DEGs) were shared across all treatments), though increased severity elicits greater differences in expression, particularly during vegetative growth. Across treatments, DEGs were highly enriched for genes related to photosynthesis and plastid maintenance. A co-expression analysis identified a single module (M8) enriched in all drought stress treatments. Genes related to drought, temperature, proline biosynthesis, and other stress responses were overrepresented in this module. In contrast to transcriptomic responses, phenotypic responses were largely divergent between early and late drought. Early-stressed sunflowers responded to drought with reduced overall growth, but became highly water-acquisitive during recovery irrigation, resulting in overcompensation (higher aboveground biomass and leaf area) and a greater overall shift in phenotypic correlations, whereas late-stressed sunflowers were smaller and more water use-efficient. Taken together, these results suggest that drought stress at an earlier growth stage elicits a change in development that enables greater uptake and transpiration of water during recovery, resulting in higher growth rates despite similar initial transcriptomic responses.

opencc-by-4.0Jun 2023View details →

Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells

The datasets analysed in the manuscript "Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells".

opencc-by-4.0Feb 2023View details →

GWAS dataset with simulated binary phenotypes for 1000 Genome Project

Phenotypes in this dataset are generated by simulating quantitative blood lipid level phenotype using the method introduced in by (https://app.terra.bio/#workspaces/amp-t2d-op/2019_ASHG_Reproducible_GWAS-V2), and binarized to be suitable as a test case for GWAS methods. ALL.shapeit2_integrated_v1a.GRCh38.20181129.phased.rsid files and allpopid.txt are the 1000 Genome Project reference data used for generating MDS plot in https://github.com/csbio/BridGE-Python

opencc-zeroJul 2023View details →

Rice phenotypic data – CNA6 population and advanced lines

One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha-1 per cycle or 67.8 kg.ha-1 per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1,128 kg.ha-1. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.