Gossypium hirsutum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA819185 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18474736_1.fastq.gz | Fastqsanger.gz | |||
| SRR18474736_2.fastq.gz | Fastqsanger.gz | |||
| SRR18474737_1.fastq.gz | Fastqsanger.gz | |||
| SRR18474737_2.fastq.gz | Fastqsanger.gz | |||
| SRR18474738_1.fastq.gz | Fastqsanger.gz |
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Project description:As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries
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Project description:High temperature (HT) stress is a major environmental stress that limits cotton growth, metabolism, and yield worldwide. The identification and characterization of thermotolerance is restricted by the plant growth environment and growth stage. In this study, four genotypes of upland cotton (Gossypium hirsutum L.) with known field thermotolerance were evaluated under normal and HTs at the seedlings stage in a growth cabinet with 11 physiological, biochemical, and phenotypic assays. Consistent with previous field observations, the thermotolerance could be identified by genotype differences at the seedling stage under HT in a growth cabinet. Comparative transcriptome analysis was performed on seedlings of two contrasting cotton genotypes after 4 and 8 hours of HT exposure. Gene ontology analysis combined with BLAST annotations revealed a large number of HT-induced differentially expressed genes (4,698) that either exhibited higher expression levels in the heat-tolerant genotype (Nan Dan Ba Di Da Hua) compared with the heat-sensitive genotype (Earlistaple 7), or were differentially expressed only in Nan Dan Ba Di Da Hua. These genes encoded mainly protein kinases, transcription factors, and heat shock proteins, which were considered to play key roles in thermotolerance in upland cotton. Two heat shock transcription factor genes (homologs of AtHsfA3, AtHsfC1) and AP2/EREBP family genes (homologs of AtERF20, AtERF026, AtERF053, and AtERF113) were identified as possible key regulators of thermotolerance in cotton. Some of the differentially expressed genes were validated by quantitative real-time PCR analysis. Our findings provide candidate genes that could be used to improve thermotolerance in cotton cultivars.
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Project description:Transcriptome data of two upland cotton and resequencing data of one upland cotton Raw sequence reads
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Project description:In this study, the leaves of upland cotton X142 and its corresponding fuzzness-lintness mutant X142fl were used as materials. Proteomic techniques were used to analysis the protein abundant between the leaves of upland cotton and MaxQuant software was selected to analyze the proteomic data.
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Project description:For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.
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