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200 results for “strawberry”
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
<p><strong>Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées</strong></p> <p>In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the <em>F. vesca</em> genome v.4.0.a2 genome. The detailed method used to obtain these results were the following:</p> <p><em>Genome sequencing and assembly NIL Fb2</em></p> <p>Genomic DNA from strawberry plants was extracted by a Hexadecyltrimethylammonium bromide (Cetrimonium bromide, CTAB) modified protocol (Healey, Furtado, Cooper, & Henry, 2014) and purified with Agencourt AMPure XP beads (cat# A63880). Long-read sequencing was performed for the genome assembly; Genomic DNA by Ligation (Oxford Nanopore, cat# SQK-LSK109) library was prepared as described by the manufacturer and sequenced on a MinION for 72 h (Oxford Nanopore).</p> <p><em>Reference genome polishing</em></p> <p>Reads obtained from nanopore were filtered with Filtlong v0.2.1 (<a href="https://github.com/rrwick/Filtlong">https://github.com/rrwick/Filtlong</a>) using --min_mean_q 80 and --min_length 200. Cleaned reads were then aligned to the most recent version of the <em>F. vesca</em> genome v4.0.a2, downloaded from the Genome Database for Rosaceae (GDR) (<a href="https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2">https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2</a>), using minimap2 v2.21 (H. Li, 2018) with parameters -aLx map-ont --MD -Y. The generated BAM file was then sorted and indexed with samtools v1.11 (H. Li et al., 2009). We used mosdepth v0.3.1 (Pedersen & Quinlan, 2018) to verify that coverage on chromosomic scaffolds was over 50 X. Sniffles v1.0.12a (Sedlazeck et al., 2018) with parameters -s 10 -r 1000 -q 20 --genotype -l 30 -d 1000 was used to detect structural variations larger than 30 bp. The VCF files obtained from Sniffles was sorted and filtered with BCFtools v1.14 (Danecek et al., 2021) to keep only structural variants (SV) with smaller than 200,00 bp (we observed that larger SV were most of the time false positive caused by misalignments in regions with gaps or Ns), supported by 10 or more reads and with allelic frequencies above 0.8 (we were interested in homozygous changes). The complete filtering command used is “bcftools view -q 0.8 -Oz -i '(SVTYPE = "DUP" || SVTYPE = "INS" || SVTYPE = "DEL" || SVTYPE = "TRA" || SVTYPE = "INV" || SVTYPE = "INVDUP") && %FILTER = "PASS" && FMT/DV>9 && SVLEN>29 && SVLEN<200000' “</p> <p>From the VCF listing all the structural variants that we detected in our <em>F. vesca </em>accession, we generated a substituted genome version based on the reference <em>F. vesca</em> genome v.4.0.a2. The reference genome was first indexed with samtools faidx v1.11(Danecek et al., 2021) and a sequence dictionary was generated with Picard CreateSequenceDictionary v2.25.6 (<a href="https://broadinstitute.github.io/picard">https://broadinstitute.github.io/picard</a>). The VCF containing the SV produced from our Nanopore sequencing was also indexed with gatk (Van der Auwera GA & O'Connor BD, 2020) IndexFeatureFile v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile">https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile</a>). FastaAlternateReferenceMaker v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker">https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker</a>) was then run with the reference genome and the VCF file to generate a substituted genome representative of our <em>Fragaria</em> accession.</p> <p>As substituting our genome with the detected structural variants changes genomic coordinates, we also corrected the public GFF genome annotation of <em>F. vesca</em> (Y, Pi, Gao, Liu, & Kang, 2019) using liftoff v1.6.1 (Shumate & Salzberg, 2021). Liftoff also detects and annotates duplications within the substituted genome.</p> <p>Transposable elements annotation was carried out using the EDTA transposable element annotation pipeline v. 1.9.6 (S. Ou et al., 2019) on the substituted genome using default parameters<em>.</em></p> <p><strong>Differentially methylated regions</strong></p> <p>The file Stress_vs_control_DMRs.zip file contains the DMRs that were called using the reads submitted to ENA (ERP135585) and obtained as follows:</p> <p>First, bedGraph files from wgbs pipeline were pre-filtered for a minimum coverage of 5 reads using awk command. These output files were then used as input for the EpiDiverse/dmr bioinformatics analysis pipeline for non-model plant species to define DMRs (Nunn <em>et al</em>., 2021) with default parameters (minimum coverage threshold 5; maximum q-value 0.05; minimum differential methylation level 10%; 10 as minimum number of Cs; Minimum distance (bp) between Cs that are not to be considered as part of the same DMR is 146 bp). The pipeline uses metilene v.0.2.6.1 (<a href="https://www.bioinf.uni-leipzig.de/Software/metilene/">https://www.bioinf.uni-leipzig.de/Software/metilene/</a>) for pairwise comparison between groups and R-packages ggplot2 v.3.3.5 and gplots v.3.1.1, for visualization results (Fig. S1). Based on our <em>F. vesca</em> genome transcript annotation and methylation data (overlapped regions with DNA methylation cytosines and DMRs), we detected the methylated genes, promoters, 3’ UTRs, 5’UTR and transposable elements in strawberry. Global DNA methylation and DMR plots were performed with R-package ggplot2. Gene analyses by methylation patterns and analysis of per-family TE DNA methylation profiles were performed with deepTools v.3.5.0 (Ramírez <em>et al</em>., 2014). DMRs comparison between treatments were done by the Venn diagram v.1.7.0 R-package.</p> <p>We produced several genome browsers tracks with DMRs that we integrated in our local instance of JBrowse available at the following url: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a></p>
Strawberry volatile organic compounds metabolomic data and QTL study
<p>This dataset contains the supplementary materials of the publication "Multivariate QTL approach reveals a major regulator of terpenoid production and other volatiles in strawberry" of the same authors. In this study we extracted volatile organic compounds from several strawberry samples and analysed their identity and abundance. We used this volatile data to perform an extensive multivariate QTL study, the results of which can be found in this dataset.</p> <p>All analysis, results and figures can be reproduced using the folder included in the <strong>supplementary data 1</strong>. If you want to reproduce part or all of our analysis, only download sup data 1. </p> <p>If you only need one of our results or data table you can download them individually:</p> <ul> <li>Sup data 2: abundances of volatile organic compounds from a biparental and diverse panel (GWAS) population.</li> <li>Sup data 3 and 4: p-value tables for all metabolites as well as multivariate traits (see publication for more information).</li> <li>Sup table 1: Summary of metabolite abundances and heritabilities across both populations.</li> <li>Sup tables 2 and 3: significant QTL signals for each trait individually and summarised per QTL locus.</li> <li>Sup table 4: previously reported VOC QTLs in strawberry, with positions imputed in the Royal Royce genome.</li> <li>Sup table 5: metadata about all the identified compounds on this and previous studies.</li> <li>Sup table 6: SNP array positions imputed in the "Royal Royce" genome assembly.</li> <li>Sup table 7: Number of markers per chromosome in this analysis.</li> </ul> <h3>Update 2025</h3> <p>We updated the underlying code and datasets to reflect several revisions made to this work. Most notably, the QTL results have been reworked. They now do not include Blink or FarmCPU results (only mixed model results, obtained through statgenGWAS). Additionally, heritability estimations, QQ-plots and other figures have been added to the reproducible results code.</p>
Epigenetic and transcriptional landscape of stress memory in woodland strawberry
<p>Bedfiles of differentially methylated regions (DMRs) that were detected in stressed mother plants (M) and their (themselves unstressed) clonal daughter plants that were formed <em>via</em> stolon formation (St1, St2, St3). The M plants were grown and sampled <em>in vitro</em> and the St1, St2, St3 plants in the green house. The DMRs were called using the the EpiDiverse/dmr bioinformatic analysis pipeline (Nunn et al., 2021).</p> <p><strong>Stress assays <em>in vitro</em></strong></p> <p>One-month-old seedlings were transferred to a fresh MS media and growth chambers at 24<sup>o</sup>C/21<sup>o</sup>C (day/night),16 h light/8 h dark, as control conditions<em>. </em>For heat-stress, plants were exposed to 30<sup>o</sup>C (day/night) for one week followed by 2 days of recovery (24<sup>o</sup>C/21<sup>o</sup>C) on fresh medium as well as the control plants. Then, the plates were transferred to 37<sup>o</sup>C (day/night) for 1 week with 2 recovery days (Figure 1A). We sampled aerial parts of plants for the molecular analyses. To reduce variability resulting from individual plants, three biological replicates of 5 pooled plants were collected per condition. Samples were harvested in 1.5 mL tubes between 9:00-11:00 a.m. and immediately frozen in liquid nitrogen and stored at -80<sup>o</sup>C until required.</p> <p><strong>Greenhouse propagation assays</strong></p> <p><em>In vitro</em> plants after heat and control treatment were transferred to soil (one plant per pot) in square plastic pots (size: 12x12x10 cm) and to a greenhouse with long day conditions (24<sup>o</sup>C/21<sup>o</sup>C day/night and 60%-70% humidity).</p> <p>Twelve mother plants (M) from control (CM; n=12) and heat-stress (HM; n=12) conditions were used for asexual propagation. From each mother plant, the two first stolons (St) were kept for producing the daughter plants of the first asexual propagation (St1) in individual pots. After two weeks, following root formation, the stolons were cut to get independent daughter plants from their mother plant (M). This process was continued until St3.</p> <p>The DMRs can also be visualized here: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a></p> <p>And the raw bisulfite sequencing data can be found here: <a href="https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585">https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585</a></p> <p> </p> <p> How many daughter plants per stolon? One stolon produce a chain of daughter plants.</p>
Figure 2 in Life table parameters of Tetranychus urticae (Trombidiformes: Tetranychidae) on four strawberry cultivars
Figure 2. Age-specific survival rate (lx), age-stage fecundity of female (fxj) and age-specific fecundity rate (mx) of Tetranychus urticae on four strawberry cultivars.
Figure 4 in Life table parameters of Tetranychus urticae (Trombidiformes: Tetranychidae) on four strawberry cultivars
Figure 4. Age-specific survivorship (lx), and fecundity (mx) of Tetranychus urticae on four strawberry cultivars.
Close range hyperspectral camera dataset with high temporal resolution of strawberry with eco-physiological data of one leaf
<p>This high temporal resolution dataset of a strawberry plant was captured in two experiments, each lasting 100h. On leaf was inserted into a leaf chamber of the LI-6400XT gas exchange system, capturing information on transpiration, photosynthesis and stomatal conductance. Environmental characteristics are also captured at canopy height. These experiments were conducted in a growth chamber at ILVO (Melle, Belgium) and only covered conditions that did not result in stress in the plant. As such, this dataset attempts to capture subtle dynamic variation in the plant.</p>
Impact of processing and storage conditions on color stability of strawberry puree: the role of PPO reactions revisited
<p>The effect of pre-heating fresh strawberries (hot break) and the use of refrigerated temperatures prior to pasteurization on the stability of anthocyanins, vitamin C, color and polyphenol oxidase (PPO) activity during storage (42 days at 35 ºC) of strawberry puree was studied. Hot break resulted in 20% residual PPO activity and caused 10% anthocyanin degradation, whereas vitamin C was unaffected. After mashing, purees were stored at 4 ºC and 25 ºC for 3 hours. During this period, anthocyanins and PPO activity remained constant independently of the processing history but ascorbic acid was oxidized faster at 25 ºC. Pasteurization caused complete inactivation of PPO, reduction of anthocyanins (25%), of <em>a*</em> value (6%) and of vitamin C (50%). Neither partial inactivation of PPO early in the processing (hot break) nor the use of refrigeration prior to pasteurization had a positive effect on color and anthocyanin stability of strawberry puree during subsequent storage, suggesting that PPO-derived reaction products formed during processing have a very limited impact on color degradation during shelf-life.</p>
[Data set]for publication Acidification of Strawberry Puree Affects Color and Volatile Characteristics during Storage
<p>Color degradation of strawberry-based products negatively affects consumer acceptance of these products. To improve the color stability of strawberry puree during storage, an acidification step (pH 1.5 and 2.5) prior to pasteurization was performed and quality changes of strawberry puree during storage (35 °C, 40 days) were monitored. Acidification prior to pasteurization resulted in an improved color and anthocyanin stability. However, the volatile fraction of strawberry puree was negatively influenced by acidification of the puree. Low acidic conditions (pH 1.5) resulted in the hydrolysis of esters, oxidation of terpene oxides, and acid-catalyzed reactions of terpene alcohols during storage. The volatile fraction of strawberry puree stored at pH 2.5 and 3.5 (the latter being the original strawberry puree) were more similar. Furthermore, after 4 days of storage, the pH of the acidified purees was brought back to the natural pH of the system (3.5) and subsequently thermally treated and stored. During this second storage, color showed a slightly faster degradation rate in those purees that were previously acidified, whereas anthocyanins exhibited similar trends suggesting that the advantage of acidification to preserve color would be beneficial after thermal processing, but more limited during storage of the regenerated product (second storage).</p>
Strawberry dataset for object detection
<p>Object detection dataset with annotated ripe and unripe strawberries and their peduncles. Data is annotated in YOLO format. Collected for: ”Real-Time CNN-based Computer Vision System for Open-Field Strawberry Harvesting Robot” <a href="https://doi.org/10.1016/j.ifacol.2022.11.109">https://doi.org/10.1016/j.ifacol.2022.11.109</a> .</p>
Data from: Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry
<p>Abstract: When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) <em>Fragaria chiloensis</em> plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a <em>Harbinger</em> transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.</p> <p>Repository content: data (sequence alignments, phylogenetic trees, genome assembly, and vcf files) and scripts associated with the manuscript "Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry"</p>
Figure 1 in Use of homeophathic preparations for red spider mite, Tetranychus urticae (Acari: Tetranychidae) control in strawberry plants
Figure 1. Degree of a) Incidence, and b) severity caused by T. urticae in strawberry plants 30 and 60 days after applying the treatments: Distilled water (Ctl); 6 and 30 CH Strawberry leaves homeopathic (Agroh); 6 and 30 CH Bovista (Bov); 6 and 30 CH Belladonna (Bellad); 6 and 30 CH Arnica (Árni) and 6 and 30 CH Ferrum sulphuricum (FS). Treatments with the same letter are not significantly different between them (p <0.05) (n = 8).
Figure 2 in First report of northern root-knot nematode, Meloidogyne hapla (Chitwood, 1949) on strawberry in Turkey
Figure 2: PCR product at 440 bp using species-specific SCAR primers (JMV1, JMV2 and JMVhapla). M: 100 bp molecular size marker, 1,2 and 3: larvae from field infected samples. +k: positive control and –k: negative control.
Fig. 5 in Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, Lower Jurassic, Strawberry Bank Lagerstätte, Somerset, UK
Fig. 5. Detail of the barnacle Toarcolepas mutans Gale and Schweigert, 2015, from upper surface of BRLSI.M3941, the Toarcian of Strawberry Bank, Somerset. In C, D, individuals are "kippered"—split along the sagittal plane. Locations of specimens on concretion shown in dashed boxes in SOM: fig. 2. Scale bars 5 mm.
Fig. 2. Fossilized driftwood association, BRLSI.M3941 in Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, Lower Jurassic, Strawberry Bank Lagerstätte, Somerset, UK
Fig. 2. Fossilized driftwood association, BRLSI.M3941, the Toarcian of Strawberry Bank, Somerset, upper surface of limestone concretion showing wood mould and associated specimens of Pseudomytiloides dubius (Sowerby, 1828) and Toarcolepas mutans Gale and Schweigert, 2015. See SOM: fig. 1 for orientation imagery.
Fig. 1 in Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, Lower Jurassic, Strawberry Bank Lagerstätte, Somerset, UK
Fig. 1. Location and stratigraphy of the Strawberry Bank Lagerstätte and associated beds. A. Location of Ilminster, Somerset, England, UK and Lower Jurassic outcrop pattern in the area. B. Limestone concretion of the Strawberry Bank Lagerstätte exposed in situ north of Ilminster during excavations of the site in 2019. Folding knife is 9 cm long. C. Stage information, and ammonite zones and subzones. D. Local lithostratigraphic scheme for the same timescale. E. Simplified sedimentary log at Strawberry Bank with the Strawberry Bank Lagerstätte shaded in pink (after Williams et al. 2015 and Boomer et al. 2021).
Fig. 4 in Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, Lower Jurassic, Strawberry Bank Lagerstätte, Somerset, UK
Fig. 4. Three dimensional rendering of the X-ray computed tomographic data of fossilized driftwood association, BRLSI.M3941 from the Toarcian of Strawberry Bank, Somerset. Dashed lines delineate the top and bottom edge of the wood mould (see SOM: fig. 1 for orientation imagery).
Fig. 3 in Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, Lower Jurassic, Strawberry Bank Lagerstätte, Somerset, UK
Fig. 3. Detail of Pseudomytiloides dubius (Sowerby, 1828) specimens from upper surface of BRLSI.M3941, Toarcian of Strawberry Bank, Somerset, showing stacking of individuals, articulation and orientation in relation to the wood. Dashed line in A marks the top edge of the wood mould. Locations of specimens on concretion correspond to numbered specimens on SOM: fig. 2 as follows: A, specimens 40 to 44; B, specimen 1; C, specimen 20; D, specimen 38.
Fig. 2 in Drosophila suzukii (Diptera: Drosophilidae) arrives at Minas Gerais State, a main strawberry production region in Brazil
Fig. 2. Damaged strawberry in the field with drosophilid flies including a Drosophila suzukii male (inlet) with its characteristic wing black dots (arrows) and 2 adults of Zaprionus indianus (white circles), scale bar = 5 mm.
Fig. 1 in Drosophila suzukii (Diptera: Drosophilidae) arrives at Minas Gerais State, a main strawberry production region in Brazil
Fig. 1. Drosophila suzukii adult female collected at Minas Gerais State, Brazil. (A) Female on a strawberry fruit in the field, scale bar = 3 mm; (B) D. suzukii egg laid inside the fruit (white box), scale bar = 5 mm; (C) oviposition hole (white circle) with the egg's spiracles (black arrow) coming out. The egg laid beneath the fruit epidermis is delimited by a white ellipse, scale bar = 500 μm; (D) the female from image A viewed under microscope, scale bar = 500 μm; and (E) the female characteristic, serrated ovipositor, scale bar = 200 μm.
Fig. 2 in A new record of a pest mite on strawberry: Phytonemus pallidus (Banks) (Acari: Tarsonemidae) arrives in Minas Gerais, Brazil
Fig. 2. Calyx of strawberry fruit infested with Phytonemus pallidus mite (A); P. pallidus eggs (B); juveniles and adults on the surface of the calyx (C); ventral view of a P. pallidus female under microscope (20×) (D); idiosoma (40×) (E); proterosoma (40×) (F).
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