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Transcriptome of Gossypium hirsutum floral and extrafloral nectaries

ABSTRACT: Transcriptome of Gossypium hirsutum floral and extrafloral nectaries

PROVIDER: PRJNA450940 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7039540_1.fastq.gz	Fastqsanger.gz
	SRR7039540_2.fastq.gz	Fastqsanger.gz
	SRR7039550_1.fastq.gz	Fastqsanger.gz
	SRR7039550_2.fastq.gz	Fastqsanger.gz
	SRR7039560_1.fastq.gz	Fastqsanger.gz

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Transcriptome of Gossypium hirsutum floral and extrafloral nectaries

Project description:Comparative RNA-Seq study of expression in Gossypium hirsutum nectaries

2018-04-19 | GSE113373 | GEO

Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

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Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase. See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).

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Project description:Nitric oxide(NO) is emerging as an important signaling molecule with diverse physiological functions in plants, leading to a necessity to discover the downstream genes and signal transduction network modulated by NO. In the current study, changes in gene expression in response to NO were studied in upland cotton(Gossypium hirsutum) using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method. After mapping to an integrated reference sequence database, we obtained about 30,000 genes per library, and yielded 2,393 differential expressed genes in total.

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