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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

ABSTRACT: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

PROVIDER: PRJNA477980 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7346990.fastq.gz	Fastqsanger.gz
	SRR7346985.fastq.gz	Fastqsanger.gz
	SRR7346986.fastq.gz	Fastqsanger.gz
	SRR7346987.fastq.gz	Fastqsanger.gz
	SRR7346988.fastq.gz	Fastqsanger.gz

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

| PRJNA477980 | ENA

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

Project description:Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and trascriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

2021-06-24 | GSE116774 | GEO

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

Project description:Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and transcriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

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Sequencing of rice degradome

Project description:miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs. Two rice samples, 3-week-old seedling and young panicles were included in the study.

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

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