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ABSTRACT: Transcriptome analysis of longan pericarp

PROVIDER: PRJNA970484 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR24474165_1.fastq.gz	Fastqsanger.gz
	SRR24474165_2.fastq.gz	Fastqsanger.gz
	SRR24474166_1.fastq.gz	Fastqsanger.gz
	SRR24474166_2.fastq.gz	Fastqsanger.gz
	SRR24474167_1.fastq.gz	Fastqsanger.gz

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Project description:To improve the gene annotation and address a series of biological questions, we generated 490,502,822 clean reads of RNA-Seq data from nine tissue types of 'sijimi' longan, including root, stem, leaf, flower_bud, flower, young fruit, pericarp, pulp, and seed, and used them for mapping, and annotation of the longan genome sequence. About 53.55 ~79.40 % of the unique RNA sequences from nine RNA-seq data could be mapped to the genome. RNA-Seq data confirmed a majority of annotated introns, identified thousands of novel alternatively spliced mRNA isoforms, extend gene, SNP and indel, indicative of more functional variation than represented by the gene set alone, and a collection of potentially new and longan-specific gene. A comparative analysis of differential expression in the gene family at the nine different developmental stages showed that most of significant differentially expressed genes were mainly involved in the metabolic pathway, plant- pathogen interaction, and biosynthesis of secondary metabolities, which was fully consistent with the standpoint of D. longan specise containing a lot of plant pahtogen resistant genes, and in particular containing high levels of polyphenolic compounds

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Project description:Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programs that are characteristic to each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types and especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of genes differentially expressed when comparing ploidy levels at a specific developmental stage. We found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation, and gene expression patterns in the tomato pericarp.

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