Ontology highlight
ABSTRACT:
PROVIDER: PRJNA717285 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14071836_1.fastq.gz | Fastqsanger.gz | |||
| SRR14071836_2.fastq.gz | Fastqsanger.gz | |||
| SRR14071837_1.fastq.gz | Fastqsanger.gz | |||
| SRR14071837_2.fastq.gz | Fastqsanger.gz | |||
| SRR14071838_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. Strawberry is one of the most economically important fruit throughout the world.Although miRNAs have been extensively studied in the past five years, limited systematic study of miRNAs has been performed on the Fragaria genus. These results show that regulatory miRNAs exist in agronomically important strawberry and may play an important role in strawberry growth, development, and response to disease. High throughput sequencing was employed to identify miRNAs in strawberry and try to describe their functions in strawberry growth and development
2012-01-04 | E-GEOD-34813 | biostudies-arrayexpress
Project description:In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. Strawberry is one of the most economically important fruit throughout the world.Although miRNAs have been extensively studied in the past five years, limited systematic study of miRNAs has been performed on the Fragaria genus. These results show that regulatory miRNAs exist in agronomically important strawberry and may play an important role in strawberry growth, development, and response to disease.
2012-01-04 | GSE34813 | GEO
Project description:The pink-flowered strawberry is very popular in China due to its appreciation and economic benefits and its flower has rich red petal with varying degrees, which is provided by anthocyanins accumulation. To better understand the functions of miRNAs, sRNAome, transcriptome and degradome sequencing were used to explore the target genes of miRNAs in flower development and coloring of pink-flowered strawberry. Nine small RNA libraries and a mixed degradome library from flower petals at different developmental stages were constructed and sequenced in this study. A total of 739 known miRNAs and 964 newly identified miRNAs were identified via small RNA sequencing, and their 2816 target genes were cleaved by 639 miRNAs based on the degradome data. There were 317 different expression miRNAs among flower development in pink-flowered strawberry regulated 2134 different expression target genes, which significantly enriched in the transcriptional regulation, phenylpropanoid biosynthesis and plant hormone signal transduction. Furthermore, integrated microRNAomic and transcriptomic analyses suggested that 98 miRNAs were targeted several transcription factors related to anthocyanin accumulation, in which 26 were targeted to MYBs, 12 bHLHs, 14 NACs, and 19 SPLs. And that, twenty seven different expression miRNAs may affect anthocyanin biosynthesis by regulating 23 targets participated in hormone signal transduction pathway in pink-flowered strawberry. The qRT-PCR analysis confirmed the expression changes of 21 miRNA-target pairs showed an opposite trend. Moreover, a co-expression regulatory network was constructed based on differentially expressed miRNA-targets according to the degradome data. Overall, we conducted a comparative analysis uncovered the regulatory functions of microRNAs in flower development and color changes of pink-flowered strawberry via multiple factors, including anthocyanin biosynthesis, hormone signaling and regulation factors. This work not only expands the knowledge of miRNAs affecting the coloration in strawberry, but also provides rich resources for future functional studies.
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Project description:For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.
2021-05-17 | GSE167183 | GEO
Project description:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
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Project description:Strawberry is economically important and widely grown but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, gene expression of both plant and bacteria in planta was analyzed at two time points, 12- and 29-days post inoculation, in order to compare pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28’588 known genes in strawberry and 4’046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most of X. fragariae genes involved in host interactions, recognitions and pathogenesis, were lower expressed at late-phase infection. This study gives a first insight on the interaction of X. fragariae with its host. The strawberry plant changed its metabolism consistently with the progression of infection.
2020-08-25 | GSE150636 | GEO
Project description:To identify miRNAs involved in senescence of strawberry fruit, two independent small RNA libraries and one degradome library from strawberry fruits stored at 20 M-BM-0C for 0 and 24 h were constructed. A total of 18,759,735 and 20,293,492 mappable small RNA sequences were generated in the two small RNA libraries, respectively, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 94 miRNAs were up-regulated and 64 were down-regulated in the senescence of strawberry fruit. Through degradome sequencing, 103 targets cleaved by 19 known miRNAs families and 55 new candidate miRNAs were identified. 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence. sample 1: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 0; sample 2: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 24 h
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Project description:To identify miRNAs involved in senescence of strawberry fruit, two independent small RNA libraries and one degradome library from strawberry fruits stored at 20 °C for 0 and 24 h were constructed. A total of 18,759,735 and 20,293,492 mappable small RNA sequences were generated in the two small RNA libraries, respectively, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 94 miRNAs were up-regulated and 64 were down-regulated in the senescence of strawberry fruit. Through degradome sequencing, 103 targets cleaved by 19 known miRNAs families and 55 new candidate miRNAs were identified. 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence.
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Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.
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