DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
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ABSTRACT:
PROVIDER: PRJEB50996 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8684940_1.fastq.gz | Fastqsanger.gz | |||
| ERR8684940_2.fastq.gz | Fastqsanger.gz | |||
| ERR8684950_1.fastq.gz | Fastqsanger.gz | |||
| ERR8684950_2.fastq.gz | Fastqsanger.gz | |||
| ERR8684931_1.fastq.gz | Fastqsanger.gz |
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Project description:Environmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes, especially at the level of DNA methylation (5-methylcytosine). DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. We investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable ecologically relevant environmental conditions at the DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in the non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. These findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses.
| S-EPMC9533225 | biostudies-literature
Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.
2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress
Project description:In this RNA-seq study, we compared the transcriptome of three Fragaria vesca genotypes in response to Phytophthora cactorum. The goal of our study was to dissect the resistance mechanism of the diploid strawberry (F. vesca) that are resistant to P. cactorum. A susceptible genotype (NCGR1218) and two resistant (NCGR1603 and Bukammen) F. vesca genotypes were used for the comparative transcriptome analyses. Plants were inoculated with P. cactorum zoospores (2mL of 2 × 105 spores/mL) in the crown (rhizome) and sampled 48 hours later. The appropriate controls for each genotype were i) samples wounded and inoculated with water and sampled 48 hours after the treatment and ii) untreated samples. Four biological replicates, each consisting of four individual test plants from each genotype were used for the transcriptome study. All the samples were collected from the crown, flash-frozen in liquid nitrogen and stored at -80 °C until RNA isolation. Total RNA was isolated using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer’s instructions. For sequencing, the libraries were prepared using the TruSeqTM stranded total RNA library prep kit (Illumina, USA), indexed and pooled, and sequenced in four lanes using the Illumina HiSeq 3/4000 (2×150 bp) System by the Norwegian Sequencing Centre, Oslo, Norway. Raw reads were quality filtered, de novo assembled into transcripts and were analysed for differentially expressed genes between the inoculated and control samples.
2023-01-01 | E-MTAB-12152 | biostudies-arrayexpress
Project description:The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
| S-EPMC3326587 | biostudies-literature
Project description:Crown rot (Phytophthora cactorum) causes significant economic losses in strawberry production. The best control strategy would be to use resistant cultivars, but polygenically inherited resistance makes the breeding of the garden strawberry (Fragaria × ananassa) challenging. The diploid wild strawberry Fragaria vesca Hawaii 4 genotype was shown previously to have resistance against crown rot. To explore the resistance mechanisms, we inoculated the roots of Hawaii 4 with P. cactorum in a novel in vitro hydroponic system to minimize interference caused by other microbes. Major reprogramming of the root transcriptome occurred, involving 30% of the genes. The surveillance system of the plant shifted from the development mode to the defense mode. Furthermore, the immune responses as well as many genes involved in the biosynthesis of the defense hormones jasmonic acid, ethylene and salicylic acid were up-regulated. Several major allergen-like genes encoding PR-10 proteins were highly expressed in the inoculated plants, suggesting that they also have a crucial role in the defense responses against P. cactorum. Additionally, flavonoids and terpenoids may be of vital importance, as several genes involved in their biosynthesis were up-regulated. The cell wall biosynthesis and developmental processes were down-regulated, possibly as a result of the down-regulation of the key genes involved in the biosynthesis of growth-promoting hormones brassinosteroids and auxin. Of particular interest was the expression of potential resistance genes in the recently identified P. cactorum resistance locus RPc-1. These new findings help to target the breeding efforts aiming at more resistant strawberry cultivars.
| S-EPMC4982697 | biostudies-literature
Project description:BackgroundWoodland strawberry (Fragaria vesca) infected with Strawberry vein banding virus (SVBV) exhibits chlorotic symptoms along the leaf veins. However, little is known about the molecular mechanism of strawberry disease caused by SVBV.MethodsWe performed the next-generation sequencing (RNA-Seq) study to identify gene expression changes induced by SVBV in woodland strawberry using mock-inoculated plants as a control.ResultsUsing RNA-Seq, we have identified 36,850 unigenes, of which 517 were differentially expressed in the virus-infected plants (DEGs). The unigenes were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The KEGG pathway analysis of these genes suggested that strawberry disease caused by SVBV may affect multiple processes including pigment metabolism, photosynthesis and plant-pathogen interactions.ConclusionsOur research provides comprehensive transcriptome information regarding SVBV infection in strawberry.
| S-EPMC4942977 | biostudies-literature
Project description:Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1.The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae ( http://www.rosaceae.org/ ). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results.Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.
| S-EPMC4318131 | biostudies-literature
Project description:The woodland strawberry, Fragaria vesca is a model fruit for a number of rosaceous crops. We have engineered altered concentrations of anthocyanin in F. vesca, to determine the impact on plant growth and fruit quality. Anthocyanin concentrations were significantly increased by over-expression or decreased by knock-down of the R2R3 MYB activator, MYB10. In contrast, a potential bHLH partner for MYB10 (bHLH33) did not affect the anthocyanin pathway when knocked down using RNAi constructs. Metabolic analysis of fruits revealed that, of all the polyphenolics surveyed, only cyanidin, and pelargonidin glucoside, and coumaryl hexose were significantly affected by over-expression and knock down of MYB10. Using the F. vesca genome sequence, members of the MYB, bHLH, and WD40 families were examined. Global analysis of gene expression and targeted qPCR analysis of biosynthetic genes and regulators confirmed the effects of altering MYB10 expression, as well as the knock-down of bHLH33. Other members of the MYB transcription factor family were affected by the transgenes. Transient expression of strawberry genes in Nicotiana benthamiana revealed that MYB10 can auto-regulate itself, and potential repressors of MYB10. In tobacco, MYB10's activation of biosynthetic steps is inhibited by the strawberry repressor MYB1.
| S-EPMC4237049 | biostudies-literature