Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [degradome]

ABSTRACT: Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [degradome]

PROVIDER: PRJNA433876 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [degradome]

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs of rose. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in rose by analyzing 10 small RNA profiles from roots, petals, pollens, stamens, and leaves. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 4000 putative targets of the conserved miRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, at least 171 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose.

2019-12-31 | GSE110494 | GEO

Analysis of microRNAs, phased small interfering RNAs and their functions in Rosa rugosa Thunb

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in rose. Here we carried out computational and experimental analysis of miRNAs, phased small interfering RNAs (phasiRNAs) and mRNAs in rose by analyzing 10 small RNA sequencing profiles from roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals of rose. To identify the targets of miRNAs and phasiRNAs, we produced a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 19,000 putative targets of the conserved miRNAs/tasiRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, 592 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. Our results also suggest that the deregulated genes in leaves and petals are significantly enriched in GO and KEGG pathways related to metabolic processes and photosynthesis. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose.

2019-12-31 | GSE113148 | GEO

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [ncRNA-seq]

2019-12-31 | GSE110490 | GEO

Analysis of microRNAs, phased small interfering RNAs and their functions in Rosa rugosa Thunb

Project description:Analysis of microRNAs, phased small interfering RNAs and their functions in Rosa rugosa Thunb

| PRJNA450264 | ENA

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb

Project description:Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb

| PRJNA433953 | ENA

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [ncRNA-seq]

Project description:Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [ncRNA-seq]

| PRJNA433859 | ENA

Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-12-31 | GSE110542 | GEO

Rosa rugosa

Project description:Rosa rugosa overview

| PRJNA558125 | ENA

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [degradome]

Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

2018-05-23 | GSE102029 | GEO

Rosa rugosa cultivar:Bao White

Project description:Rosa rugosa cultivar:Bao White Raw sequence reads

| PRJNA498442 | ENA