RNA-Seq data of fruit development across ten species
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB86778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14710200_1.fastq.gz | Fastqsanger.gz | |||
| ERR14710200_2.fastq.gz | Fastqsanger.gz | |||
| ERR14710300_1.fastq.gz | Fastqsanger.gz | |||
| ERR14710300_2.fastq.gz | Fastqsanger.gz | |||
| ERR14710201_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa. Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array.
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Project description:Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Chili pepper is an economically and culturally important horticultural crop as well as a good model for the study of secondary metabolism during fruit development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. Results RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueno 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. Subsets of genes were expressed only at a single time point sampled (1,278, 1,596, 1,519 and 1,583 genes at 10, 20, 40 and 60 DAA, respectively). We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. Conclusions In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.
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Project description:Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa. Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array. Eggplant plants were was grown under controlled conditions in glasshouse. Flowers were hand-pollinated at anthesis and samples were collected at 0, 5, 10, 20 and 50 days post anthesis (dpa). Total RNA was isolated using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturerM-bM-^@M-^Ys protocol. Affymetrix tomato GeneChip Genome array (Affymetrix, USA) having 10,000 probe sets was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).
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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: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.
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Project description:With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.
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