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ABSTRACT: transcriptome data of self- and cross- pollination ovary after 48h in Schima superba

PROVIDER: PRJNA625576 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11551253_1.fastq.gz	Fastqsanger.gz
	SRR11551253_2.fastq.gz	Fastqsanger.gz
	SRR11551254_1.fastq.gz	Fastqsanger.gz
	SRR11551254_2.fastq.gz	Fastqsanger.gz
	SRR11551255_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in leaves of two subtropical trees grown under contrasting light

Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.

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Grain gene expression profile at early developmental stage

Project description:Gene expression profiling of ovary at 1-10 days and embryo at 4-10 days after flowering (DAT) was performed to obtain an overall signature of the rice transcriptome during early grain development. After the onset of pollination, ovary samples at 1-10 DAT and embryo samples at 4-10 DAT with two replicates were collected and used for microarray analysis. A total of 20 microarray data for ovary and 14 microarray data for embryo were obtained.

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Project description:Schima superba restriction site-associated DNA sequencing

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Transcriptome analysis of 103 RILs of a B73 x H99 RIL population

Project description:The RIL population used in this study is derived from a cross between parental lines B73 and H99, followed by 12 generations of self-pollination. In total 142 RILs were generated and 223 markers were used for mapping these RILs (Marino et al. (2009) Mol Genet Genomics, 281:163-179). The transcriptome of a randomly chosen subset of 103 RILs was analyzed in this study using RNA-seq.

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Project description:Sexual reproduction in flowering plants involves intimate interactions between the growing pollen tube and the female reproductive structure. These interactions start immediately after pollen landing on the stigma and continue during the pollen tube journey through the style and the ovary. Thus, well before fertilization, genes in the gynoecium are affected by the growing pollen tubes. Genes activated at a distance in the ovary before pollen tubes arrival represent one class of such genes. Using a global transcriptomic approach, expression profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations revealed that these pollinations are perceived differently from a distance in the ovary. As the pollen tubes grew along the style, more and more genes became specific for each pollination type, although even early on when no difference could be observed in pollen tube growth rates, each pollination type already displayed its specific signature. Wounding experiments as well as methyl jasmonate treatment were also conducted to determine if transmitting tissue cell death caused by pollen tube growth in the style could also activate gene expression at distance in the ovary. Our data suggest that pollen tube growth in the style is at least partially perceived as a wounding aggression, and that a SI pollination is more akin to a wound response than the other pollination type tested, suggesting similarities in the signaling pathways controlling pollen recognition and stress responses. More importantly, our transcriptomic analysis reveals a highly specific recognition of various pollination types that is relayed from a distance to the ovary ahead of fertilization.

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