Comparative Transcriptome Analysis Uncovers the Regulatory Functions of MicroRNAs in Flower Development and Color Changes of Pink-flowered Strawberry
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ABSTRACT:
PROVIDER: PRJNA796538 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17576414.fastq.gz | Fastqsanger.gz | |||
| SRR17576415.fastq.gz | Fastqsanger.gz | |||
| SRR17576416.fastq.gz | Fastqsanger.gz | |||
| SRR17576417.fastq.gz | Fastqsanger.gz | |||
| SRR17576418.fastq.gz | Fastqsanger.gz |
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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:Pink-flowered strawberry is a new promising ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, prolonged flowering period and edible fruits. However, the transcriptional events underlying anthocyanins biosynthesis pathway have not been fully characterized in its petal coloration. The pigment compounds accumulated in its fruits were the same as cultivated strawberry, but different from in its flowers. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed an integrated analyses of the transcriptome and metabolomes involved in red petals at three development stages (Bud stage (L), Coloration beginning stage (Z) and Big bud stage (D)) of pink-flowered strawberry. Transcript and metabolite profiles were generated through high-throughput RNA-sequencing and high-performance liquid chromatography coupled with mass spectrometry, respectively. The results showed that the main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compounds. There were no anthocyanins detected in white-flowered hybrids. A total of 50 285 non-redundant unigenes were obtained from the transcriptome databases, among which 59 differentially expressed genes could be identified as putative homologues of flower coloration related genes. Based on a comprehensive analysis relating pigmentation compounds to gene expression profiles, the mechanism of flower color formation was examined in pink-flowered strawberry. Furthermore, a new hypothesis explaining the lack of color phenotype of the white-flowered strawberry hybrids from the level of the transcriptome. The expression patterns of FpDFR gene and FpANS gene corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink; Whereas other anthocyanin biosynthesis genes were weakly related flower color deepened. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the key factors that lead to the inability to accumulate anthocyanins in the white petals of PFS hybrids. Meanwhile, the competitive effect of FpFLS gene and FpDFR gene may further inhibit anthocyanin synthesis. The data presented herein are important for understanding of the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating into novel genes that are potential targets for breeding new valuable pink-flowered strawberry cultivars.
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Project description:Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry
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Project description:Study on Cyanidin Metabolism in Flower colors of Pink-flowered Strawberry Based on Transcriptome Sequencing and Metabolite Analysis
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Project description:Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry one library was constructed and sequenced
2014-09-01 | E-GEOD-44930 | biostudies-arrayexpress
Project description:The pink-flowered strawberry is popular in China due to its high ornamental value. In the present study, sRNAome, transcriptome, and degradome sequencing were performed to understand the functions of microRNAs (miRNAs) and their target genes during flower development in pink-flowered strawberry. Nine small RNA libraries and a mixed degradome library from flower petals at different developmental stages were constructed and sequenced. A total of 739 known miRNAs and 964 novel miRNAs were identified via small RNA sequencing, and 639 miRNAs were identified to cleave 2,816 target genes based on the degradome data. Additionally, 317 differentially expressed miRNAs among the various stages of flower development were identified, which regulated 2,134 differentially expressed target genes. These target genes were significantly enriched in the transcriptional regulation, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. Furthermore, integrated microRNAomic and transcriptomic analyses suggested that 98 miRNAs targeted several transcription factors, including MYBs (26), bHLHs (12), NACs (14), and SPLs (19), related to anthocyanin accumulation. In addition, 27 differentially expressed miRNAs might affect anthocyanin biosynthesis by regulating 23 targets involved in the hormone signal transduction pathway. The quantitative real-time PCR (qRT-PCR) analysis confirmed the expression changes of 21 miRNA-target pairs. Furthermore, the transient expression of candidate miRNAs was performed in the pink-flowered strawberry cultivar "Fenyun" at the bud stage. Introduction of FamiR156a, FamiR396e, and FamiR858_R-2 in the "Fenyun" increased flower color intensity, while transient expression of FamiR828a decreased flower color intensity. Overall, the present study uncovers the regulatory functions of microRNAs, including anthocyanin biosynthesis, hormone signaling, and regulation factors during flower development and coloration in pink-flowered strawberry. This work expands the knowledge of miRNAs affecting coloration in strawberry and provides rich resources for future functional studies.
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Project description:We have performed a transcriptome analysis of genes at three different ripening stages of the pink-white fruits and the ripe stage of the red fruits of Chinese bayberry. This analysis provided a total of 119,701 unigenes, of which 41.43% were annotated in the Nr database. Our results showed that the formation of the pink-white color in Chinese bayberry fruits depended on the anthocyanin metabolic pathway, regulated by MYB1. Downregulated expression of key anthocyanin biosynthetic pathway genes, such as UFGT, F3’H, and ANS at the late stage of fruits development compared with DK3 fruits resulted in the failure to form red fruits. Our findings shed light on the regulatory mechanisms and metabolic processes that control color development in the fruits of Chinese bayberry.
2018-10-09 | GSE120925 | GEO
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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