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Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination

ABSTRACT: Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination

PROVIDER: PRJNA495618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7994050.fastq.gz	Fastqsanger.gz
	SRR7994060.fastq.gz	Fastqsanger.gz
	SRR7994070.fastq.gz	Fastqsanger.gz
	SRR7994080_1.fastq.gz	Fastqsanger.gz
	SRR7994080_2.fastq.gz	Fastqsanger.gz

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Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination

Project description:Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. Of these miRNAs, 32, 74 and 61 miRNAs were responsive to drought, heat and their combination, respectively. Following degradome sequencing, 50 sequences were identified as targets of 34 miRNAs in tomatoes at combined stress. Moreover, 467 circRNAs were identified in the 12 samples.

2020-02-20 | GSE121089 | GEO

MicroRNA profiles in leaves of Sorghum exposed to drought or heat or their combination

Project description:MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.

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Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes.

Project description:Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.

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Project description:Human circular RNAs can function in competing endogenous RNA (ceRNA) network by sponging miRNA and regulating gene expression. Viruses are evolved to regulate noncoding RNAs such as miRNAs and circRNAs to facilitate their propagation and pathogenesis. Studies on how host ceRNAs upon human coronavirus infection were scarce, and the functions of circRNAs during the infection of Middle East respiratory syndrome coronavirus (MERS-CoV) has not been deeply revealed. Therefore, we conducted a whole transcriptional profile (RNA-seq) analysis to compare the expression of circRNAs, miRNAs and mRNAs between the mock-infected and MERS-CoV-infected human lung adenocarcinoma (Calu-3) cells. Integrated analysis of ceRNAs revealed putative viral pathogenic circRNAs induced by MERS-CoV and their interplay with miRNAs and genes. Our study offered new insights into the mechanisms of interplays of MERS-CoVs and hosts, and established a model promising to be applied to other coronavirus or other viruses for the identification of novel host factors.

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