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MiR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

ABSTRACT: miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

OTHER RELATED OMICS DATASETS IN: GSE48346

PROVIDER: PRJNA209731 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR922416.fastq.gz	Fastqsanger.gz
	SRR922417.fastq.gz	Fastqsanger.gz

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Similar Datasets

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

Project description:Rice was domesticated independently in Asia and Africa, leading to two distinct but closely related crop species, Oryza sativa and Oryza glaberrima, respectively. The two domestications lead to morphological changes, in which a higher branching complexity of the panicles, influencing seed production and crop yield. Although much emphasis was placed on changes in transcriptional regulation during rice domestication and improvement, no large-scale study of small RNA regulation changes during domestication has been reported so far. To analyze whether rice domestication has altered the expression of small RNAs, we performed deep sequencing of small RNA transcriptomes from early developmental stages of panicles from 10 genotypes of the cultivated African species and 10 genotypes of its wild-relative O. barthii. Our study shows a drastic expression change of the 21-nucleotide smallRNA population. A total of 29% of these smallRNAs are overexpressed in panicles of O. barthii vs. O. glaberrima, corresponding mainly to 21-nucleotide phased siRNAs (or phasiRNAs). We also show that these changes are associated with a differential expression of a known regulator of phased siRNAs, miR2118 during early panicle development. Finally, these changes are associated to a heterochronic alteration of phasiRNAs and miR2118 expression pattern, during panicle development with a delayed expression in the domesticated species. Our study suggests a major reshaping of the regulation network from a specific class of small RNA during African rice domestication.

2016-04-18 | GSE48346 | GEO

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.

Project description:BackgroundRice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii.ResultsOur RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems.ConclusionDifferential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.

| S-EPMC4788661 | biostudies-literature

Down-regulated expression of OsDCL3b affects small RNA biogenesis and panicle development in rice

Project description:Two types of small (18-24 nt) non-coding RNAs (ncRNAs), microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been found to exist widely in higher plants. OsDCL3b has just been reported to process the 24-nt phased small RNAs in rice, which are preferentially expressed in panicle. In this study, we find that down-regulated expression of OsDCL3b leads to lower pollen sterility and seed setting rate, which results in decreased grain yield per plant in rice. Next, small RNA and mRNA sequencing were performed to study the decrease of pollen fertility and seed setting rate. 942 differentially expressed genes were identified, and some of them have already been known to be involved in rice panicle development. Our results indicate that there is a close correlation between small RNA and rice yield.

2019-04-12 | GSE102747 | GEO

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs.

Project description:BackgroundIn plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed.ResultsHere, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB .ConclusionsIn summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

| S-EPMC8120726 | biostudies-literature

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]

Project description:Plants evolved an array of disease resistance genes (R genes) to fight pathogens. In the absence of pathogen infection, NBS-LRR genes, which comprise a major subfamily of R genes, are suppressed by a small RNA cascade involving microRNAs (miRNAs) that trigger the biogenesis of phased siRNAs (phasiRNAs) from R gene transcripts. However, whether or how R genes influence small RNA biogenesis is unknown. In this study, we isolated a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and traced the defects to the over accumulation and nuclear localization of an R protein SNC1. We showed that nuclear SNC1 represses the transcription of miRNA and phasiRNA loci, probably through the transcriptional corepressor TPR1. Intriguingly, nuclear SNC1 reduces the accumulation of phasiRNAs from three source R genes and concomitantly, the expression of a majority of the ~170 R genes was up-regulated. Taken together, this study reveals a new R gene-miRNA-phasiRNA regulatory module that regulates plants' growth-defense trade-off.

2018-10-09 | GSE111238 | GEO

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]

Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]

| PRJNA436256 | ENA

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]

2018-10-09 | GSE111239 | GEO

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

| PRJNA436243 | ENA

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]

Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]

| PRJNA436260 | ENA

bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage

Project description:Whole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage The aim of this study was to identify candidate genes responsible for grain number per panicle by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 20 differentially expressed genes, respectively. The differentially expressed genes were shorted to 4 on the basis of their occurance in the QTL region (responcible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.

2010-01-01 | GSE17169 | GEO

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