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ABSTRACT: Genome-wide identification and functional analysis of GhFAR gene family in cotton

PROVIDER: PRJNA672231 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12904552_1.fastq.gz	Fastqsanger.gz
	SRR12904552_2.fastq.gz	Fastqsanger.gz
	SRR12904553_1.fastq.gz	Fastqsanger.gz
	SRR12904553_2.fastq.gz	Fastqsanger.gz
	SRR12904554_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis combined with metabolome analysis reveals the significant functions of CesA genes in cotton (Gossypium hirsutum) fiber length development

Project description:Cotton (Gossypium hirsutum) is widely distributed worldwide, and improving the quality of its fiber is one of the most important tasks in cotton breeding. Cotton fibers are primarily composed of cellulose, which is synthesized and regulated by cellulose synthase (CesAs). However, the molecular mechanism of CesA genes in cotton is unclear. In this study, the cotton transcriptome and metabolome were used to investigate the significant function of CesA genes in fiber development. Finally, 321 metabolites were obtained, 84 of which were associated with the corresponding genes. Interestingly, a target gene named Gh_A08G144300, one of the CesA gene family members, was closely correlated with the development of cotton fibers. Then, identification and functional analysis were conducted. The target CesA gene Gh_A08G144300 was selected and analysed to determine its specific function in cotton fiber development. High-level gene expression of Gh_A08G144300 was found at different fiber development stages by RNA-seq analysis, and the silencing of Gh_A08G144300 visibly inhibited the growth of cotton fibers, showing that it is critical for their growth. This study provides an important reference for research on the gene function of Gh_A08G144300 and the regulatory mechanism of fiber development in cotton.

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Project description:Genome-wide identification and analysis of WRKY gene family in jute

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Project description:Genome wide identification of the RhoGAP gene family and functional analysis of OsRhoGAP2 in seed germination of rice

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Project description:Functional Characterization of GhCNGCs Family in Upland Cotton

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TR accompanied with the study titled A multicenter phase II study of Nivolumab monotherapy in recurrent and/or metastatic gastrointestinal cancer patients with high Tumor Mutation Burden (TMB-H).

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Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.

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Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

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