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ABSTRACT: male and female date palm sequencing

PROVIDER: PRJNA433966 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR6716030_1.fastq.gz	Fastqsanger.gz
	SRR6716030_2.fastq.gz	Fastqsanger.gz
	SRR6716031_1.fastq.gz	Fastqsanger.gz
	SRR6716031_2.fastq.gz	Fastqsanger.gz
	SRR6716026_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose: To identify conserved and novel miRNAs in date palm and, most importantly, to identify miRNAs that could play a role in salt tolerance Methods: we generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm,then Deep sequencing of these four sRNA libraries,last The bioinformatics analysis,further validated using semi-quantitative PCR (qPCR). Results: Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of most miRNAs in date palm. In leaves, all of the identified miRNAs were affected by the salinity treatment, and the majority (75%) of them were upregulated, whereas in roots, only 33% of the miRNAs were upregulated, but 44% of them were downregulated, while the remaining miRNAs (22%) were unaffected by the treatment. The salt responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, and calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world with a wide range of abiotic stress tolerance, date palm contains a large population of conserved and nonconserved miRNAs that function at the posttranscriptional level. Conclusions: This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.

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Project description:Simple Markov model. There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal. The yearly transition probabilities are: Healthy to Dead: 0.01; Healthy to Sick: 0.2 for Male and 0.1 for Female; Sick to Healthy: 0.1; Sick to Dead: 0.3. The transition probability now depends on the cohort (Male or Female) and can be expressed as a function of a Boolean covariate Male. Initial conditions: Healthy = (50 Male, 50 Female), Sick = (0,0) and Dead = (0,0). Output: Number of men and women in each disease state for years 1-10.

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