XbAmeMedi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB80831 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR13762720.fastq.gz | Fastqsanger.gz | |||
| ERR13766898_1.fastq.gz | Fastqsanger.gz | |||
| ERR13766898_2.fastq.gz | Fastqsanger.gz |
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Project description:Americardia media (Atlantic strawberry cockle), genomic and transcriptomic data
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Project description:Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry
2014-09-01 | GSE44930 | GEO
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:Breeding day-neutral strawberry (Fragaria x ananassa Duchesne) is pivotal to extend fruit-bearing season and increase the efficiency of production. However, genetic improvement of day-neutrality by the means of molecular marker technologies remains slow due to genome complexity of octoploid strawberry. This study employs an innovative approach by integrating the Subtracted Diversity Array (SDA) technology and Bulked Segregant Analysis (BSA) to facilitate the identification of molecular markers associated with day-neutrality in octoploid strawberry. A Fragaria Discovery Panel (FDP) containing 287 features specific to strawberry genome was constructed as a platform for rapid screening of DNA polymorphism between one short day (SD) strawberry DNA bulk and three day-neutral (DN) bulks varrying in flowering strength. Differential array hybridisation patterns between the DN and SD bulks revealed a novel molecular marker, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. Interestingly, a 12 bp deletion was observed within the FaP2E11 sequence cloned from SD genotypes but not DN genotypes. As cytokinin is required to induce flowering, this result indicates that full sequence of FaP2E11 and the sequence with deletion are allelic variants linked to the low enzyme activity CKX1 and the wild type alleles, respectively.
2017-02-09 | GSE70145 | GEO
Project description:Strawberry cultivation is associated with high mineral fertilizer doses and excessive use of chemical plant protection products. Based on previous research, we expected that chitin application to the growing medium will increase the nutrient availability and activate the plant’s systemic defense response, resulting in higher strawberry yields and less disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin induced the plant’s shoot biomass, explained by elevated N concentration in the growing medium and/or the attraction of plant-growth promoting fungal genera towards the plant root, such as Mortierella and Umbelopsis. The over-excessive N concentration and P and K deficiencies in the chitin treatment led to nutrient disbalances. This may explain the decreased fruit yield and disease resistance of the fruits towards Botrytis cinerea. In contrast, chitin caused a clear defense priming effect of the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in less disease symptoms. Chitin caused positive effects on shoot growth and disease resistance of the leaves, but caution needs to be taken for nutrient disbalances leading to negative influences on fruit production and disease susceptibly.
2021-01-01 | GSE144526 | GEO
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:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
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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.
2022-04-20 | GSE193522 | 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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