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ABSTRACT: Global transcriptome analyses of peanut seeds

PROVIDER: PRJNA685603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13263256.fastq.gz	Fastqsanger.gz
	SRR13263257.fastq.gz	Fastqsanger.gz
	SRR13263258.fastq.gz	Fastqsanger.gz
	SRR13263259.fastq.gz	Fastqsanger.gz
	SRR13263260.fastq.gz	Fastqsanger.gz

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Project description:peanut seeds RNA-seq

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Comparative transcriptomic analysis of the roots of intercropped maize by microarray

Project description:Intercropping is a vital technology in resource-limited agricultural systems with low inputs. Peanut/maize intercropping enhances iron (Fe) nutrition in calcareous soil. Proteomic studies of the differences in peanut leaves, maize leaves and maize roots between intercropping and monocropping systems indicated that peanut/maize intercropping not only improves Fe availability in the rhizosphere but also influences the levels of proteins related to carbon and nitrogen metabolism. Moreover, intercropping may enhance stress resistance in the peanut plant (Xiong et al. 2013b). Although the mechanism and molecular ecological significance of peanut/maize intercropping have been investigated, little is known about the genes and/or gene products in peanut and maize roots that mediate the benefits of intercropping. In the present study, we investigated the transcriptomes of maize roots grown in intercropping and monocropping systems by microarray analysis. The results enabled exploration differentially expressed genes in intercropped maize. Peanut (Arachis hypogaea L. cv. Luhua14) and maize (Zea mays L. cv. Nongda108) seeds were grown in calcareous sandy soil in a greenhouse. The soil was enhanced with basal fertilizers [composition (mg·kg−1 soil): N, 100 (Ca (NO3)2·4H2O); P, 150 (KH2PO4); K, 100 (KCl); Mg, 50 (MgSO4·7H2O); Cu, 5 (CuSO4·5H2O); and Zn, 5 (ZnSO4·7H2O)]. The experiment consisted of three cropping treatments: peanut monocropping, maize monocropping and intercropping of peanut and maize. After germination of peanut for 10 days, maize was sown. Maize samples were harvested after 63 days of growth of peanut plants based on the degree of Fe chlorosis in the leaves of monocropped peanut. The leaves of monocropped peanut plants exhibited symptoms of Fe-deficiency chlorosis at 63 days, while the leaves of peanut plants intercropped with maize maintained a green color.

2017-01-24 | GSE93771 | GEO

Transcriptome and proteome analysis of resistant peanut pre-harvest seeds in response to Aspergillus flavus

Project description:In this study, we used RNA-seq to obtain and compare transcriptomic profiles of a resistant genotype J11 in pre-harvest seeds, with A. flavus inoculation at the whole-genome level. The TMT method was also implemented to help further understand the molecular mechanism of peanut resistance to A. flavus invasion at proteome level. Meanwhile, we conducted a thorough research on a chitinase and a NBS-LRR gene, which were found in our data. This study is our first step towards a comprehensive genome-scale platform for developing Aspergillus resistant peanut cultivars through genetic engineering.

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Project description:Transcriptome analyses on seeds developed in different parental conditions investigating the effect of the parental environment on the transcriptome of dry seeds of three different genotypes

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Peanut oral immunotherapy suppresses clonally distinct subsets of T helper cells

Project description:Food allergy affects an estimated 8% of children in the US, with increasing severity and global prevalence. Using single-cell RNA sequencing and paired TCR sequencing, we assessed the transcriptomes of CD154+ and CD137+ peanut-reactive T helper cells from 12 peanut-allergic patients longitudinally throughout peanut oral immunotherapy. These results demonstrate a differential response to OIT among subsets of peanut-reactive T helper cells, and indicate that non-Th2 activation signatures may be associated with clinical outcomes.

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Small RNA and Degradome Deep Sequencing Reveals the roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.)

Project description:Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering ( DAF ) in two peanut 8th generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.

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Project description:Peanut allergy reaction severity correlates with increased intestinal epithelial cell (IEC) barrier permeability. CC027/GeniUnc mice develop peanut allergy by intragastric administration of peanut proteins without adjuvant. We report that peanut-allergic CC027/GeniUnc mice showed increased IEC barrier permeability and systemic peanut allergen Ara h 2 after challenge. Jejunal epithelial cell transcriptomics showed effects of peanut allergy on IEC proliferation, survival, and metabolism, and revealed IEC-predominant angiopoietin like-4 (Angptl4) as a unique feature of CC027/GeniUnc peanut allergy. Peanut-allergic pediatric patients demonstrated significantly higher serum ANGPTL4 compared to non-peanut-allergic but atopic patients, highlighting its potential as a biomarker of peanut allergy.

2021-07-09 | GSE179595 | GEO

Combined transcriptome and translatome analyses reveal a role for tryptophan dependent auxin biosynthesis in the control of DOG1 dependent seed dormancy

Project description:Transcriptome and translatome analyses of 6 and 24 hours imbibed seeds dormant and non-dormant seeds of NILDOG1-Cvi with and without addition of the transcription inhibitor Cordycepin. NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006).

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Project description:Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. The array SNP data was used for revaling of key candidate loci and genes associated with important agronomic traits in peanut

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